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Moncayo M, Teran E, Reyes J, Yerovi G, Robalino M, Aguilar AC, Garzon-Chavez D. Identification of the Genotypes Circulating in the Ecuadorian Population Infected with the Hepatitis C Virus (HCV). Risk Manag Healthc Policy 2023; 16:1403-1409. [PMID: 37554251 PMCID: PMC10406119 DOI: 10.2147/rmhp.s412599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/08/2023] [Indexed: 08/10/2023] Open
Abstract
INTRODUCTION The hepatitis C virus (HCV) is responsible for 1.5 million new infections, and around 290 thousand deaths worldwide. 15 to 30% of the patients that go into a chronic phase of the disease will develop cirrhosis or hepatocellular carcinoma within 20 years and is the leading etiology for liver transplantation. HCV genetic characteristics display a remarkable genetic diversity, which divides HCV into 8 genotypes and 67 subgenotypes; the treatment and probability of chronic HCV depend on these genotypes and subgenotypes. In Ecuador, there is no available information regarding HCV genotypes and subgenotypes; therefore, this study aims to provide an overview of the main genotypes circulating in Ecuador. METHODS In a cross-sectional and descriptive study using the Ecuadorian Ministry of Health (MSP) registry of patients already diagnosed with Hepatitis C (HCV) between 2017 and 2019. From 51 patients identified by health ministry, blood samples from a total of 15 subjects (named HCV1 to HCV15) were collected using an appropriate venipuncture technique. Pandemic-related circumstances avoid reaching all patients identified by health ministry. RESULTS After the amplification of 11 samples from patients living in the Ecuadorian territory, the genotypes of HCV obtained were distributed as follows: 6 samples corresponding to subgenotype 2b (54.5%), 2 samples corresponding to subgenotype 1a (18.2%), 2 samples corresponding to subgenotype 4d (18.2%) and 1 corresponding to sample 1b (9.1%). CONCLUSION These results represent the first epidemiological approach to genotype distribution in Ecuador, and it contributes to better management of patients. We emphasize the importance of the development of better strategies from the Healthcare Ministry of Ecuador (MSP) for the identification, treatment and tracking of HCV patients.
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Affiliation(s)
- Miguel Moncayo
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Laboratorio Clinico Pasteur Dr. Alberto Moncayo Calero, Quito, Ecuador
| | - Enrique Teran
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Jorge Reyes
- Facultad de Ciencias Químicas, Universidad Central del Ecuador, Quito, Ecuador
- Departamento de Microbiologı´a, Hospital del IESS Quito Sur, Quito, Ecuador
| | | | | | - Ana Cristina Aguilar
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Daniel Garzon-Chavez
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito USFQ, Quito, Ecuador
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Li M, Lv Y, Cui D, Xu Y, Lin M, Zhang X, Wang Y, Shen C, Xie J. Development and clinical validation of a one-step pentaplex real-time reverse transcription PCR assay for detection of hepatitis virus B, C, E, Treponema pallidum, and a human housekeeping gene. BMC Infect Dis 2023; 23:358. [PMID: 37231355 DOI: 10.1186/s12879-023-08240-w] [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: 12/09/2022] [Accepted: 04/11/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND With the safety of blood transfusion being a major public health concern, the development of a rapid, sensitive, specific, and cost-effective multiplex PCR assay for simultaneous detection of hepatitis B virus(HBV), hepatitis C virus (HCV), hepatitis E virus (HEV), and Treponema pallidum(T. pallidum) in blood is crucial. METHODS Five primer pairs and probes were designed towards conserved regions of target genes and used to establish a one-step pentaplex real-time reverse transcription PCR(qRT-PCR) assay for simultaneous detection of HBV, HCV, HEV, T. pallidum, and RNase P(housekeeping gene), providing sample quality check. The clinical performance of the assay was further determined with 2400 blood samples from blood donors and patients in Zhejiang province, and compared the results with commercial singleplex qPCR and serological assays. RESULTS The 95% limit of detection(LOD) of HBV, HCV, HEV, and T. pallidum were 7.11 copies/µL, 7.65 copies/µL, 8.45 copies/µL, and 9.06 copies/µL, respectively. Moreover, the assay has good specificity and precision. Compared to the singleplex qPCR assay, the novel assay for detecting HBV, HCV, HEV, and T. pallidum presented 100% clinical sensitivity, specificity, and consistency. Several discrepant results between serological and pentaplex qRT-PCR assays were found. Of 2400 blood samples, there were 2(0.08%) HBsAg positive samples, 3(0.13%) anti-HCV positive samples, 29(1.21%) IgM anti-HEV positive samples and 6(0.25%) anti-T. pallidum positive samples proven negative in nucleic acid detection. 1(0.04%) HBV DNA positive sample and 1(0.04%) HEV RNA positive sample were detected negative by serological testing. CONCLUSIONS The developed pentaplex qRT-PCR is the first assay on simultaneous, sensitive, specific, and reproducible detection of HBV, HCV, HEV, T. pallidum, and RNase P in a single tube. It could detect pathogens in blood during the window period of infection and is a good tool for effectively screening blood donors and early clinical diagnosis.
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Affiliation(s)
- Miaomiao Li
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yan Lv
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Dawei Cui
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yushan Xu
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Mengjiao Lin
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | | | - Yongjun Wang
- Key Laboratory of Blood Safety Research of Zhejiang Province, Zhejiang Province Blood Center, Hangzhou, 310052, China
| | - Cuifen Shen
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China.
| | - Jue Xie
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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Hannula R, Söderholm J, Svendsen T, Skaland M, Nordbø SA, Steinum H, Damås JK. Hepatitis C outreach project and cross-sectional epidemiology in high-risk populations in Trondheim, Norway. Ther Adv Infect Dis 2021; 8:20499361211053929. [PMID: 34733508 PMCID: PMC8558792 DOI: 10.1177/20499361211053929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Hepatitis C is highly prevalent among people who use drugs (PWUD), and the hepatitis C virus (HCV) epidemic is less characterised in Norway. The aims of the study were to assess the prevalence and treatment willingness in high-risk populations by reaching out to frequently visited sites for high-risk populations. METHODS Individuals from high-risk populations were included from September 2015 to March 2017. Two dedicated study nurses frequently visited the local opioid substitution clinic, outpatient clinics, PWUD day centres, local prison, and refugee centre in Trondheim, Norway. Demographic data, risk behaviour, and clinical symptoms were obtained by study questionnaire. Subjects with anti-HCV+ rapid test were subsequently tested for HCV RNA and genotyped. Viraemic patients were offered referral for HCV treatment evaluation. RESULTS A total of 381 participants were included in the study: 52 immigrants, 62 prisoners, and 267 PWUD. The anti-HCV prevalence rates were 0% (n = 0) in immigrants, 40% (n = 25) in prisoners, and 61% (n = 164) in PWUD, with 24% (n = 15) of prisoners and 42% (n = 108) of PWUD being viraemic. Of those qualifying for treatment (n = 31), 30 wished to be evaluated. CONCLUSION This study showed high HCV prevalence in prisoners and PWUD and that infected high-risk patients were interested in treatment evaluation.
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Affiliation(s)
- Raisa Hannula
- Department of Infectious Diseases, Trondheim University Hospital, 7006 Trondheim, Norway
| | - Jonas Söderholm
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Therese Svendsen
- Department of Infectious Diseases, Trondheim University Hospital, Trondheim, Norway
| | - Maja Skaland
- Department of Infectious Diseases, Trondheim University Hospital, Trondheim, Norway
| | - Svein A. Nordbø
- Department of Medical Microbiology, St. Olavs Hospital HF, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Harald Steinum
- Department of Infectious Diseases, Trondheim University Hospital, Trondheim, Norway
| | - Jan K. Damås
- Department of Infectious Diseases, Trondheim University Hospital, Trondheim, Norway
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Yip CCY, Sridhar S, Lau JHN, Cheng AKW, Leung KH, Chen JHK, Chan KH, Cheng VCC, Yuen KY. Comparative performance of two commercial sample-to-result systems for hepatitis C virus quantitation and genotyping. Expert Rev Mol Diagn 2020; 20:1253-1258. [PMID: 32893699 DOI: 10.1080/14737159.2020.1820327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Accurate assays for hepatitis C virus (HCV) quantitation and genotyping are important for the management of HCV infection. In this study, we evaluated the performance of cobas HCV and cobas HCV GT assays (Roche) for HCV quantitation and genotyping on the cobas 4800 System. METHODS We compared the performance of the cobas HCV assays with another commercial system (Abbott m2000) using a panel of well-characterized patient samples and proficiency testing samples. RESULTS The limit-of-detection of the cobas HCV assay in our center was higher (15 IU/mL) than the manufacturer claim (9.2 IU/mL). The assay showed high analytical specificity, accuracy, precision, and linearity. Performance was congruent with the RealTime HCV assay (Abbott). For genotyping, the cobas HCV GT assay only showed moderate agreement with the RealTime HCV Genotype II assay (kappa = 0.550). The cobas assay outperformed the RealTime assay for typing HCV genotypes 1b and 6 (p = 0.033). CONCLUSION Our results confirm that the cobas 4800 System is a reliable platform for HCV quantitation and genotyping. The cobas HCV GT assay is a good choice for genotype 1b/6 endemic areas in east Asia, clearly outperforming the RealTime HCV Genotype II assay.
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Affiliation(s)
- Cyril C Y Yip
- Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China
| | - Siddharth Sridhar
- Department of Microbiology, The University of Hong Kong , Hong Kong Special Administrative Region, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong , Hong Kong Special Administrative Region, China.,Research Centre of Infection and Immunology, The University of Hong Kong , Hong Kong Special Administrative Region, China.,Carol Yu Centre for Infection, The University of Hong Kong , Hong Kong Special Administrative Region, China
| | - John H N Lau
- Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China
| | - Andrew K W Cheng
- Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China
| | - Kit-Hang Leung
- Department of Microbiology, The University of Hong Kong , Hong Kong Special Administrative Region, China
| | - Jonathan H K Chen
- Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong , Hong Kong Special Administrative Region, China
| | - Vincent C C Cheng
- Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China.,Department of Microbiology, The University of Hong Kong , Hong Kong Special Administrative Region, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong , Hong Kong Special Administrative Region, China.,Research Centre of Infection and Immunology, The University of Hong Kong , Hong Kong Special Administrative Region, China.,Carol Yu Centre for Infection, The University of Hong Kong , Hong Kong Special Administrative Region, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong , Hong Kong Special Administrative Region, China
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Yang X, Ding T, Huang H, Xu Y, Yu J, Chen Z. Development and validation of a simple and rapid method for hepatitis C virus genotyping based on one-step RT-qPCR. Exp Ther Med 2020; 20:2284-2290. [PMID: 32765706 DOI: 10.3892/etm.2020.8912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/22/2020] [Indexed: 11/06/2022] Open
Abstract
Hepatitis C virus (HCV) infections caused by different subtypes require different treatments; therefore, rapid and cost-effective genotyping methods for the diagnosis of HCV are greatly needed. In the present study, a new method to diagnose HCV subtypes that depends on a one-step quantitative reverse transcription PCR (RT-qPCR) and TaqMan fluorescence probe technique is described. Five pairs of primers and five probes were designed, which were able to detect five genotypes in three reaction tubes. One reaction was used to detect the 1b subtype, one was used to detect the 2a and 6a subtypes, and the other was used to detect the 3a and 3b subtypes. Rigorous performance validation was implemented for five aspects: Precision, sensitivity, accuracy, specificity and anti-interference. The HCV subtype that infected 289 patients was evaluated in the present study via RT-qPCR and verified by sequencing. The results revealed that the 1b subtype accounted for 45% of infections, the 2a subtype accounted for 9% of infections, the 3a subtype accounted for 13% of infections, the 3b subtype accounted for 18% of infections, and the 6a subtype accounted for 15% of infections. The analytical sensitivity for the detection of each of the five HCV subtypes was 1,000 IU/ml. The new method performed well in the performance validation mentioned above, indicating its effectiveness as a HCV genotyping method. RT-qPCR has mitigated some of the former challenges of existing HCV genotyping methods, including the time commitment, expense, and inaccuracy of such methods. The performance validation of this new method showed that RT-qPCR is reliable enough to be widely applied in China for HCV genotyping.
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Affiliation(s)
- Xinyun Yang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China.,The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Ting Ding
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China.,The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Haifeng Huang
- Triplex International Biosciences (China) Co., Ltd., Xiamen, Fujian 361000, P.R. China
| | - Yang Xu
- Department of First Generation Sequencing, Hangzhou DiAn Medical Laboratory, Hangzhou, Zhejiang 310030, P.R. China
| | - Jian Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Zhanguo Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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El-Tahan RR, Ghoneim AM, Zaghloul H. Dissection of two drug-targeted regions of Hepatitis C virus subtype 4a infecting Egyptian patients. Virus Genes 2020; 56:564-581. [PMID: 32572756 PMCID: PMC7307947 DOI: 10.1007/s11262-020-01776-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 06/16/2020] [Indexed: 12/11/2022]
Abstract
Recently, treatment of HCV infection has been improved after the development of direct acting antivirals (DAAs) which target different viral proteins (NS3-4A, NS5A and NS5B). The activity and effectiveness of these DAAs are affected by the presence of resistance associated substitutions (RASs). This study aimed to characterize HCV genotypes circulating among Egyptian HCV patients, to dissect the full sequences of HCV NS3-4A and NS5B regions, and to characterize RASs associated with NS3-4A and NS5B inhibitors in HCV treatment-naïve patients. Genotyping of 80 HCV samples from treatment-naïve patients was done using restriction fragment length polymorphism and phylogenetic analysis based on some full NS5B sequences. Results showed the prevalence of HCV subtype 4a. Twenty four new full sequences of NS3-4A and NS5B regions of subtype 4a were deposited in the GenBank database. In general, the substitutions associated with NS3-4A-targeting drugs were absent predicting possible responsiveness of Egyptian HCV patients to these drugs. In addition, the absence of amino acid substitutions associated with resistance to Sofosbuvir may predict good response to treatment with Sofosbuvir. Some amino acid substitutions associated with resistance to different classes of non-nucleoside inhibitors were detected. Further investigations on treated Egyptian HCV patients may evaluate the effectiveness of the massively used drugs. Many predicted T-cell-binding epitopes in NS3-4A and NS5B regions were found to be highly conserved in the currently studied isolates; a finding that might be important for HCV vaccine development. We demonstrated potential NS3 epitopes that could be used in engineering T cells against HCV epitopes.
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Affiliation(s)
- Radwa R El-Tahan
- Zoology Department, Faculty of Science, Damietta University, New Damietta, P.O. 34517, Damietta, Egypt
| | - Ahmed M Ghoneim
- Zoology Department, Faculty of Science, Damietta University, New Damietta, P.O. 34517, Damietta, Egypt.
| | - Hosam Zaghloul
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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Serdari D, Kostaki EG, Paraskevis D, Stamatakis A, Kapli P. Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV. PeerJ 2019; 7:e7754. [PMID: 31667012 PMCID: PMC6816385 DOI: 10.7717/peerj.7754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/26/2019] [Indexed: 12/15/2022] Open
Abstract
Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.
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Affiliation(s)
- Dora Serdari
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandros Stamatakis
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics Evolution and Environment, University College London, University of London, London, United Kingdom
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Sridhar S, Yip CCY, Chan JFW, To KKW, Cheng VCC, Yuen KY. Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping. Diagn Microbiol Infect Dis 2018; 91:34-37. [PMID: 29434000 DOI: 10.1016/j.diagmicrobio.2017.12.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 12/16/2017] [Accepted: 12/29/2017] [Indexed: 01/21/2023]
Abstract
The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping.
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Affiliation(s)
- Siddharth Sridhar
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Cyril C Y Yip
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jasper F W Chan
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kelvin K W To
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Vincent C C Cheng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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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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10
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Tong YQ, Liu B, Fu CH, Zheng HY, Gu J, Liu H, Luo HB, Li Y. Genetic analysis of the PKHD1 gene with long-rang PCR sequencing. ACTA ACUST UNITED AC 2016; 36:758-766. [PMID: 27752906 DOI: 10.1007/s11596-016-1658-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/26/2016] [Indexed: 12/13/2022]
Abstract
PKHD1 gene mutations are found responsible for autosomal recessive polycystic kidney disease (ARPKD). However, it is inconvenient to detect the mutations by common polymerase chain reaction (PCR) because the open reading frame of PKHD1 is very long. Recently, long-range (LR) PCR is demonstrated to be a more sensitive mutation screening method for PKHD1 by directly sequencing. In this study, the entire PKHD1 coding region was amplified by 29 reactions to avoid the specific PCR amplification of individual exons, which generated the size of 1 to 7 kb products by LR PCR. This method was compared to the screening method with standard direct sequencing of each individual exon of the gene by a reference laboratory in 15 patients with ARPKD. The results showed that a total of 37 genetic changes were detected with LR PCR sequencing, which included 33 variations identified by the reference laboratory with standard direct sequencing. LR PCR sequencing had 100% sensitivity, 96% specificity, and 97.0% accuracy, which were higher than those with standard direct sequencing method. In conclusion, LR PCR sequencing is a reliable method with high sensitivity, specificity and accuracy for detecting genetic variations. It also has more intronic coverage and lower cost, and is an applicable clinical method for complex genetic analyses.
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Affiliation(s)
- Yong-Qing Tong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Bei Liu
- Department of Pathology, Affiliated Tianyou Hospital of Wuhan University of Science and Technology, Wuhan, 430064, China
| | - Chao-Hong Fu
- Department of Clinical Laboratory, Dongfeng Hospital, Hubei University of Medicine, Shiyan, 442008, China
| | - Hong-Yun Zheng
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jian Gu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Hang Liu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Hong-Bo Luo
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| | - Yan Li
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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11
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Marascio N, Pavia G, Strazzulla A, Dierckx T, Cuypers L, Vrancken B, Barreca GS, Mirante T, Malanga D, Oliveira DM, Vandamme AM, Torti C, Liberto MC, Focà A. Detection of Natural Resistance-Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct-Acting Antiviral Agents-Naïve Patients. Int J Mol Sci 2016; 17:E1416. [PMID: 27618896 PMCID: PMC5037695 DOI: 10.3390/ijms17091416] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/17/2016] [Accepted: 08/22/2016] [Indexed: 12/18/2022] Open
Abstract
Naturally occurring resistance-associated substitutions (RASs) can negatively impact the response to direct-acting antivirals (DAAs) agents-based therapies for hepatitis C virus (HCV) infection. Herein, we set out to characterize the RASs in the HCV1b genome from serum samples of DAA-naïve patients in the context of the SINERGIE (South Italian Network for Rational Guidelines and International Epidemiology, 2014) project. We deep-sequenced the NS3/4A protease region of the viral population using the Ion Torrent Personal Genome Machine, and patient-specific majority rule consensus sequence summaries were constructed with a combination of freely available next generation sequencing data analysis software. We detected NS3/4A protease major and minor variants associated with resistance to boceprevir (V36L), telaprevir (V36L, I132V), simeprevir (V36L), and grazoprevir (V36L, V170I). Furthermore, we sequenced part of HCV NS5B polymerase using Sanger-sequencing and detected a natural RAS for dasabuvir (C316N). This mutation could be important for treatment strategies in cases of previous therapy failure.
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Affiliation(s)
- Nadia Marascio
- Department of Health Sciences, Institute of Microbiology, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy.
- Katholieke Universiteit (KU) Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, 3000 Leuven, Belgium.
| | - Grazia Pavia
- Department of Health Sciences, Institute of Microbiology, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy.
| | - Alessio Strazzulla
- Department of Medical and Surgical Sciences, Unit of Infectious and Tropical Diseases, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy.
| | - Tim Dierckx
- Katholieke Universiteit (KU) Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, 3000 Leuven, Belgium.
| | - Lize Cuypers
- Katholieke Universiteit (KU) Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, 3000 Leuven, Belgium.
| | - Bram Vrancken
- Katholieke Universiteit (KU) Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, 3000 Leuven, Belgium.
| | - Giorgio Settimo Barreca
- Department of Health Sciences, Institute of Microbiology, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy.
| | - Teresa Mirante
- Centro di Servizio Interdipartimentale (CIS)-Genomica funzionale e Patologia Molecolare, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy.
| | - Donatella Malanga
- Department of Experimental and Clinical Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy.
| | - Duarte Mendes Oliveira
- Department of Experimental and Clinical Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy.
| | - Anne-Mieke Vandamme
- Katholieke Universiteit (KU) Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, 3000 Leuven, Belgium.
- Center for Global Health and Tropical Medicine, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal.
| | - Carlo Torti
- Department of Medical and Surgical Sciences, Unit of Infectious and Tropical Diseases, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy.
| | - Maria Carla Liberto
- Department of Health Sciences, Institute of Microbiology, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy.
| | - Alfredo Focà
- Department of Health Sciences, Institute of Microbiology, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy.
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