1
|
Osiowy C, Giles E, Lowe CF, Matic N, Murphy DG, Uzicanin S, Drews SJ, O'Brien SF. Hepatitis B virus genotype surveillance in Canadian blood donors and a referred patient population, 2016-2021. Vox Sang 2024; 119:232-241. [PMID: 38141175 DOI: 10.1111/vox.13568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/06/2023] [Accepted: 11/05/2023] [Indexed: 12/25/2023]
Abstract
BACKGROUND AND OBJECTIVES Hepatitis B virus (HBV) genotypes (A-H) have a distinct geographic distribution and are highly associated with the country of birth. Canada has experienced increased immigration over the past decade, primarily from regions where HBV is endemic. This study investigated the proportions and trends of HBV genotypes within blood donor and clinical populations of Canada over the period 2016-2021. MATERIALS AND METHODS Study samples involved two cohorts: (1) Canadian blood donors (n = 246) deferred from donation due to HBV test positivity and (2) chronic HBV patients from across Canada (clinically referred population, n = 3539). Plasma or serum was extracted, and the surface antigen and/or polymerase-coding region was amplified and sequenced to determine genotype by phylogenetic analysis. RESULTS Six (A-E, G) and eight (A-H) HBV genotypes were detected among deferred blood donors and the clinically referred population, respectively. Differences in HBV genotype proportions between the two cohorts were observed across Canada. Males comprised most of the referred population among genotypes A-E (p < 0.0001), except for genotypes B and C. The median age was younger among blood donors (36 years [range 17-72]) compared with the referred population (41 years [range 0-99]). Distinct trends of increasing (E, referred; B, blood donor) and decreasing genotype prevalence were observed over the study period. CONCLUSION HBV genotypes in Canada are highly diverse, suggesting a large immigrant population. Observed trends in genotype prevalence and proportional differences among cohorts imply shifts among the HBV-infected population of Canada, which warrants continued surveillance.
Collapse
Affiliation(s)
- Carla Osiowy
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Elizabeth Giles
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Christopher F Lowe
- St. Paul's Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nancy Matic
- St. Paul's Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Donald G Murphy
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | | | - Steven J Drews
- Canadian Blood Services, Edmonton, Alberta, Canada
- Division of Diagnostic and Applied Microbiology, Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sheila F O'Brien
- Canadian Blood Services, Ottawa, Ontario, Canada
- School of Epidemiology & Public Health, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
2
|
Unmasking a hepatitis C genotype 3a/1b dual infection in an individual treated with elbasvir/grazoprevir. J Hepatol 2023; 78:e95-e96. [PMID: 36435298 DOI: 10.1016/j.jhep.2022.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/02/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022]
|
3
|
Zitha T, Chen CY, Mudawi H, Hussein W, Mukhtar M, Shigidi M, Yousif MEA, Ali MA, Glebe D, Kramvis A. Molecular characterization and genotyping of hepatitis C virus from Sudanese end-stage renal disease patients on haemodialysis. BMC Infect Dis 2022; 22:848. [PMCID: PMC9661773 DOI: 10.1186/s12879-022-07833-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background
Hepatitis C virus (HCV) is a global public health problem, with ~ 11 million people in Africa infected. There is incomplete information on HCV in Sudan, particularly in haemodialysis patients, who have a higher prevalence compared to the general population. Thus, our objectives were to genotype and molecularly characterize HCV isolated from end-stage renal disease haemodialysis patients.
Methods
A total of 541 patients were recruited from eight haemodialysis centres in Khartoum and screened for anti-HCV. Viral loads were determined using in-house real-time PCR in seropositive patients. HCV was genotyped and subtyped using sequencing of amplicons of 5′ untranslated (UTR) and non-structural protein 5B (NS5B) regions, followed by phylogenetic analysis of corresponding sequences.
Results
The HCV seroprevalence in the study was 17% (93/541), with HCV RNA-positive viremic rate of 7% (40/541). A low HCV load, with a mean of 2.85 × 104 IU/ml and a range of 2.95 × 103 to 4.78 × 106 IU/ml, was detected. Phylogenetic analyses showed the presence of genotypes 1, 3, 4, and 5 with subtypes 1a, 1b, 1 g, 3a, 4a, 4 l, 4 m, 4 s, and 4t. Sequences of HCV from the same haemodialysis units, clustered in similar genotypes and subtypes intimating nosocomial infection.
Conclusion
HCV infection is highly prevalent in haemodialysis patients from Sudan, with phylogenetic analysis intimating nosocomial infection. HCV genotyping is useful to locate potential transmission chains and to enable individualized treatment using highly effective direct-acting antivirals (DAAs).
Collapse
|
4
|
Gökahmetoğlu S, Polat C, Atalay MA, Sezgin GC, Ergör G, Aygen B, Gürsoy Ş, Hakan Abacıoğlu Y, Abacioglu YH. Healthcare-Related HCV Genotype 4d Infections in Kayseri, Turkey. THE TURKISH JOURNAL OF GASTROENTEROLOGY : THE OFFICIAL JOURNAL OF TURKISH SOCIETY OF GASTROENTEROLOGY 2022; 33:964-970. [PMID: 36098364 PMCID: PMC9797710 DOI: 10.5152/tjg.2022.21822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND The frequency of genotype 4 hepatitis C virus infection is significantly higher in a city compared to other provinces in Turkey. In this study, we aimed to investigate the epidemiology and risk factors of hepatitis C virus genotype 4 infection in Kayseri province of Turkey. METHODS A case-control study was conducted with 61 hepatitis C virus genotype 4-infected patients and 71 controls. A questionnaire was administered to the patients and controls, asking for information about the risk factors of hepatitis C virus transmission. Core/ E1 and NS5B regions of hepatitis C virus genome were amplified and sequenced by Sanger method. Phylogenetic analysis and molecular clock analysis were performed. The risk was determined by calculating the odds ratio and 95% CI. Logistic regression analysis was performed to determine the effect of risk factors by controlling for confounding variables. RESULTS Kayseri isolates were closely related to type 4d sequences but formed a separate cluster. According to the molecular clock analysis, hepatitis C virus genotype 4d entered Kayseri province probably between 1941 and 1988. Blood transfusion and surgical intervention were found to be significant risk factors for the infection. CONCLUSION Epidemiological data showed that hepatitis C virus genotype 4d infections are significantly associated with unsafe medical procedures.
Collapse
Affiliation(s)
- Selma Gökahmetoğlu
- Department of Medical Microbiology, Erciyes University Faculty of Medicine, Kayseri, Turkey,Corresponding author: Selma Gökahmetoğlu, e-mail:
| | - Ceylan Polat
- Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Mustafa Altay Atalay
- Department of Medical Microbiology, Erciyes University Faculty of Medicine, Kayseri, Turkey
| | - Gülten Can Sezgin
- Department of Gastroenterology, Erciyes University Faculty of Medicine, Kayseri, Turkey
| | - Gül Ergör
- Department of Public Health, Dokuz Eylül University Faculty of Medicine, İzmir, Izmir, Turkey
| | - Bilgehan Aygen
- Department of Infectious Diseases, Erciyes University Faculty of Medicine, Kayseri, Turkey
| | - Şebnem Gürsoy
- Department of Gastroenterology, Erciyes University Faculty of Medicine, Kayseri, Turkey
| | - Yusuf Hakan Abacıoğlu
- Department of Medical Microbiology, İzmir University of Economics Faculty of Medicine, İzmir, Turkey
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Christensen KT, Pierard F, Beuselinck K, Bonsall D, Bowden R, Lagrou K, Nevens F, Schrooten Y, Simmonds P, Vandamme AM, Van Wijngaerden E, Dierckx T, Cuypers L, Van Laethem K. Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort. J Clin Virol 2022; 155:105252. [DOI: 10.1016/j.jcv.2022.105252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 02/07/2023]
|
6
|
Antuori A, Montoya V, Piñeyro D, Sumoy L, Joy J, Krajden M, González-Gómez S, Folch C, Casabona J, Matas L, Colom J, Saludes V, Martró E. Characterization of Acute HCV Infection and Transmission Networks in People Who Currently Inject Drugs in Catalonia: Usefulness of Dried Blood Spots. Hepatology 2021; 74:591-606. [PMID: 33609288 DOI: 10.1002/hep.31757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND AND AIMS Accurate identification of recent HCV infections is critical for tracing the extent and mechanisms of ongoing transmission. We aimed to validate dried blood spot (DBS) samples for the assessment of Hepatitis C virus (HCV) genetic diversity and to determine epidemiological parameters including incidence, determinants of acute infection, and phylogenetic clustering in people who inject drugs (PWID). APPROACH AND RESULTS HCV nonstructural protein 5B next-generation sequencing was performed from plasma and/or DBS in 220 viremic PWID from the HepCdetect II study. No significant differences were found in consensus sequences or Shannon entropy (SE) intrahost diversity estimate between paired plasma/DBS specimens. SE values were used to identify acute infections with 93.3% sensitivity (95% CI, 0.81-1.06) and 95.0% specificity (95% CI, 0.88-1.02) in a set of well-defined controls. An acute HCV infection (either primary infection or reinfection) was detected in 13.5% of viremic participants and was associated with age ≤30 years (OR, 8.09), injecting less than daily (OR, 4.35), ≤5 years of injected drug use (OR, 3.43), sharing cocaine snorting straws (OR, 2.89), and being unaware of their HCV status (OR, 3.62). Annualized HCV incidence was estimated between 31 and 59/100 person-years. On phylogenetic analysis, 46.8% of viremic cases were part of a transmission pair or cluster; age ≤30 years (OR, 6.16), acute infection (OR, 5.73), and infection with subtype 1a (OR, 4.78) were independently associated with this condition. CONCLUSIONS The results obtained from plasma and DBS characterize PWID with acute infection and those involved in ongoing HCV transmission and allow estimating incidence from cross-sectional data. This information is critical for the design and assessment of targeted harm reduction programs and test-and-treat interventions and to facilitate monitoring of HCV elimination in this key population.
Collapse
Affiliation(s)
- Adrián Antuori
- Microbiology DepartmentLaboratori Clínic Metropolitana NordHospital Universitari Germans Trias i PujolInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolBadalonaSpain
- Genetics and Microbiology DepartmentUniversitat Autònoma de BarcelonaBellaterraSpain
| | | | - David Piñeyro
- High Content Genomics & Bioinformatics UnitInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolProgram of Predictive and Personalized Medicine of CancerBadalonaSpain
| | - Lauro Sumoy
- High Content Genomics & Bioinformatics UnitInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolProgram of Predictive and Personalized Medicine of CancerBadalonaSpain
| | - Jeffrey Joy
- BC Centre for Excellence in HIVVancouverBCCanada
- Department of MedicineUniversity of British ColumbiaVancouverBCCanada
| | - Mel Krajden
- Public Health LaboratoryHepatitis-Clinical Prevention Services British Columbia Centre for Disease ControlVancouverBCCanada
| | - Sara González-Gómez
- Microbiology DepartmentLaboratori Clínic Metropolitana NordHospital Universitari Germans Trias i PujolInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolBadalonaSpain
| | - Cinta Folch
- Centre for Epidemiological Studies on Sexually Transmitted Infections and HIV/AIDS of CataloniaPublic Health Agency of CataloniaBadalonaSpain
- Group 27Biomedical Research Networking Centre in Epidemiology and Public HealthInstituto de Salud Carlos IIIMadridSpain
| | - Jordi Casabona
- Centre for Epidemiological Studies on Sexually Transmitted Infections and HIV/AIDS of CataloniaPublic Health Agency of CataloniaBadalonaSpain
- Group 27Biomedical Research Networking Centre in Epidemiology and Public HealthInstituto de Salud Carlos IIIMadridSpain
| | - Lurdes Matas
- Microbiology DepartmentLaboratori Clínic Metropolitana NordHospital Universitari Germans Trias i PujolInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolBadalonaSpain
- Genetics and Microbiology DepartmentUniversitat Autònoma de BarcelonaBellaterraSpain
- Group 27Biomedical Research Networking Centre in Epidemiology and Public HealthInstituto de Salud Carlos IIIMadridSpain
| | - Joan Colom
- Programme for Prevention, Control and Treatment of HIVSTIs and Viral HepatitisPublic Health Agency of CataloniaBarcelonaSpain
| | - Verónica Saludes
- Microbiology DepartmentLaboratori Clínic Metropolitana NordHospital Universitari Germans Trias i PujolInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolBadalonaSpain
- Genetics and Microbiology DepartmentUniversitat Autònoma de BarcelonaBellaterraSpain
- Group 27Biomedical Research Networking Centre in Epidemiology and Public HealthInstituto de Salud Carlos IIIMadridSpain
| | - Elisa Martró
- Microbiology DepartmentLaboratori Clínic Metropolitana NordHospital Universitari Germans Trias i PujolInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolBadalonaSpain
- Genetics and Microbiology DepartmentUniversitat Autònoma de BarcelonaBellaterraSpain
- Group 27Biomedical Research Networking Centre in Epidemiology and Public HealthInstituto de Salud Carlos IIIMadridSpain
| |
Collapse
|
7
|
Hepatitis C Virus Subtypes Novel 6g-Related Subtype and 6w Could Be Indigenous in Southern Taiwan with Characteristic Geographic Distribution. Viruses 2021; 13:v13071316. [PMID: 34372521 PMCID: PMC8310057 DOI: 10.3390/v13071316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) genotype (GT) 6 is the most genetically diverse GT and mainly distributed in Southeast Asia and south China but not Taiwan. Earlier studies showed the major HCV GTs in Taiwan were GT 1b and 2 with very rare GT 6 except in injection drug users (IDUs), and subtype 6a is the main GT 6 subtype among IDUs. Recently, we reported a much higher prevalence (18.3%) of GT 6 in Tainan City, southern Taiwan. This study was designed to clarify the subtypes of GT 6 in this endemic area. A total of 3022 (1343 men and 1679 women) HCV viremic patients were enrolled. Subtypes of GT 6 were determined by sequencing of core/E1 and nonstructural protein 5B in 322 of 518 GT 6 patients. The overall GT 6 prevalence rate was 17.1% (518/3022), with higher prevalence districts (>25%) located in northern Tainan. A novel 6g-related subtype is the most prevalent subtype (81.0%), followed by 6w (10.8%), 6a (7.5%), and 6n (0.7%). The high GT 6 prevalence in Tainan was mainly due to a novel 6g-related subtype and 6w. These two subtypes could be indigenous in Tainan with characteristic geographic distribution.
Collapse
|
8
|
Cunningham EB, Hajarizadeh B, Amin J, Hellard M, Bruneau J, Feld JJ, Cooper C, Powis J, Litwin AH, Marks P, Dalgard O, Conway B, Moriggia A, Stedman C, Read P, Bruggmann P, Lacombe K, Dunlop A, Applegate TL, Matthews GV, Fraser C, Dore GJ, Grebely J. Reinfection Following Successful Direct-acting Antiviral Therapy for Hepatitis C Virus Infection Among People Who Inject Drugs. Clin Infect Dis 2021; 72:1392-1400. [PMID: 32166305 DOI: 10.1093/cid/ciaa253] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/10/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The aim of this analysis was to calculate the incidence of hepatitis C virus (HCV) reinfection and associated factors among 2 clinical trials of HCV direct-acting antiviral treatment in people with recent injecting drug use or currently receiving opioid agonist therapy (OAT). METHODS Participants who achieved an end-of-treatment response in 2 clinical trials of people with recent injecting drug use or currently receiving OAT (SIMPLIFY and D3FEAT) enrolled between March 2016 and February 2017 in 8 countries were assessed for HCV reinfection, confirmed by viral sequencing. Incidence was calculated using person-time of observation and associated factors were assessed using Cox proportional hazard models. RESULTS Seventy-three percent of the population at risk of reinfection (n = 177; median age, 48 years; 73% male) reported ongoing injecting drug use. Total follow-up time at risk was 254 person-years (median, 1.8 years; range, 0.2-2.8 years). Eight cases of reinfection were confirmed for an incidence of 3.1/100 person-years (95% confidence interval [CI], 1.6-6.3) overall and 17.9/100 person-years (95% CI, 5.8-55.6) among those who reported sharing needles/syringes. Younger age and needle/syringe sharing were associated with HCV reinfection. CONCLUSIONS These data demonstrate the need for ongoing monitoring and improved strategies to prevent HCV reinfection following successful treatment among people with ongoing injecting drug use to achieve HCV elimination. CLINICAL TRIALS REGISTRATION NCT02336139 and NCT02498015.
Collapse
Affiliation(s)
- Evan B Cunningham
- The Kirby Institute, University of New South Wales Sydney, Sydney, Australia
| | - Behzad Hajarizadeh
- The Kirby Institute, University of New South Wales Sydney, Sydney, Australia
| | - Janaki Amin
- The Kirby Institute, University of New South Wales Sydney, Sydney, Australia.,Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Margaret Hellard
- The Burnet Institute, Melbourne, Australia.,Department of Infectious Disease, The Alfred Hospital, Melbourne, Australia
| | - Julie Bruneau
- Centre Hospitalier de l'Université de Montréal, Montreal, Canada
| | | | | | - Jeff Powis
- South Riverdale Community Health Centre, Toronto, Canada
| | - Alain H Litwin
- Albert Einstein College of Medicine, New York, New York, USA
| | - Philippa Marks
- The Kirby Institute, University of New South Wales Sydney, Sydney, Australia
| | | | - Brian Conway
- Vancouver Infectious Diseases Center, Vancouver, Canada
| | - Alberto Moriggia
- Fondazione Epatocentro Ticino, Lugano, Switzerland.,Ingrado Addiction Services, Lugano, Switzerland
| | - Catherine Stedman
- Christchurch Hospital and University of Otago, Christchurch, New Zealand
| | - Phillip Read
- The Kirby Institute, University of New South Wales Sydney, Sydney, Australia.,Kirketon Road Centre, Sydney, Australia
| | | | - Karine Lacombe
- Inserm UMR-S1136, Sorbonne Université, Hôpital Saint-Antoine, Paris, France
| | - Adrian Dunlop
- Newcastle Pharmacotherapy Service, Newcastle, Australia
| | - Tanya L Applegate
- The Kirby Institute, University of New South Wales Sydney, Sydney, Australia
| | - Gail V Matthews
- The Kirby Institute, University of New South Wales Sydney, Sydney, Australia.,St Vincent's Hospital, Sydney, Australia
| | - Chris Fraser
- Coolaid Community Health Centre, Victoria, Canada
| | - Gregory J Dore
- The Kirby Institute, University of New South Wales Sydney, Sydney, Australia.,St Vincent's Hospital, Sydney, Australia
| | - Jason Grebely
- The Kirby Institute, University of New South Wales Sydney, Sydney, Australia
| |
Collapse
|
9
|
Ullah S, Ali M, Shaheen A, Zia F, Rahman L, Rahman S, Ali H, Din M, Waris A, Shinwari ZK. Sofosbuvir Resistance-associated Substitutions in the Palm Domain of HCV-NS5B RNA Dependent RNA Polymerase; Study of two Sofosbuvir non-responders. Int J Infect Dis 2021:S1201-9712(21)00426-4. [PMID: 34000421 DOI: 10.1016/j.ijid.2021.05.025] [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: 01/14/2021] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE In current study we performed sequencing of palm domain of HCV-NS5B gene, its ancestral analysis along with amino acids substitution analysis. These analysis were done to find the molecular basis of the viral resistance against Sofosbuvir drug. METHODS Blood samples from individuals with chronic Hepatitis C infection that were resistant to Sofosbuvir were collected. The samples were processed for their molecular characterization that included RNA extraction, Complementary DNA (cDNA) synthesize, nested PCR, gel elution, Sequencing, ancestral and 3D structure analysis. RESULTS Evolutionary analysis revealed that current study sequences (QAU-01, QAU-02) clustered with a previously studied sequence, KY971494.1. Moreover, we reports multiple novel amino acid substitutions in the palm domain of NS5B gene such as Ile116Val, Asn117Gly, Glu246Ala, Val252Ala, Glu258Gln, Cys262Leu, Ser269Arg, Ala272Thr, Ile293Leu, Lys304Arg, Asn307Gly, Ala338Val and Arg345Gly in our query sequence (QAU-01). At 246 and 269 position in (QAU-02), no substitution was observed. CONCLUSIONS We have noticed that the current sequences are relatively emerging and could have been originated from aforementioned sequence recently. Based on the current results, we suggests that these substitutions could be associated with structural or functional impairment of protein and could also be may be considered as resistance associated substitutions (RAS) to Sofosbuvir drug.
Collapse
Affiliation(s)
- Sana Ullah
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Asmat Shaheen
- Department of Biochemistry, Khyber Medical University-Institute of Medical Sciences, Kohat, Pakistan.
| | - Fatima Zia
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Lubna Rahman
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Sidra Rahman
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Hammad Ali
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Misbahud Din
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Abdul Waris
- Department of Biotechnology, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| | - Zabta Khan Shinwari
- Department of Plant Sciences, Quaid-i-Azam University Islamabad, 45320, Pakistan.
| |
Collapse
|
10
|
Cheng XD, Xu HF, Wei F, Jiang LX, Zhou HZ. The genotype analysis of the hepatitis C virus in Heilongjiang Province, China. Medicine (Baltimore) 2021; 100:e25203. [PMID: 33950918 PMCID: PMC8104223 DOI: 10.1097/md.0000000000025203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 02/25/2021] [Indexed: 01/04/2023] Open
Abstract
Introduction: Hepatitis C virus (HCV) infection is a major public health issue. HCV genotype identification is clinically important to tailor the dosage and duration of treatment, and recombination in intra-patient populations of HCV may lead to the generation of escape mutants, as previously observed for other RNA viruses. Up to now, there is no study assessing HCV genotypes and subtypes in Heilongjiang Province, China.Methods: To determine genotype and phylogenetic analysis of HCV in Heilongjiang Province is crucial. In this study, we amplified 3 genome regions (5'UTR, E1, and NS5B) of 30 HCV patients in Heilongjiang Province, amplified products were analyzed by bioinformatics.Results: We found that 23 specimens had concordant subtypes in the 3 gene regions (2a and 1b), 7 HCV patients were considered the recombinants, the recombination pattern of the 7 HCV patients in the 5'UTR, E1, and NS5B region as followed: 1b/2a/1b, 2a/2a/1b, 1b/2a/2a, 1b/2a/1b, 1b/2a/1b, 1b/2a/1b, 2a/2a/1b.Conclusions: The findings in the present study showed that a higher recombination rate (23%) than other researches, and the recombination of 2a/1b in the 5'UTR, E1, and NS5B region was only found in the present study up to now.
Collapse
Affiliation(s)
- Xue-Di Cheng
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, Shandong
- Department of Laboratory Diagnosis, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Hua-Feng Xu
- Department of Laboratory Diagnosis, Heilongjiang Provincial Hospital
| | - Feng Wei
- Department of Laboratory Diagnosis, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Li-Xin Jiang
- Department of Laboratory Diagnosis, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Hai-Zhou Zhou
- Department of Laboratory Diagnosis, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| |
Collapse
|
11
|
Agarwal R, Gupta E, Kumar G, Singh KK, Sharma MK. Evaluation of true point of care molecular assay using fingerstick capillary whole blood for diagnosis of hepatitis C infection. J Med Microbiol 2021; 70. [PMID: 33704042 DOI: 10.1099/jmm.0.001332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
At present, the available point of care (POC) molecular assays for hepatitis C are not considered as true POC due to sample collection and processing requiring minimal laboratory infrastructure. A new POC Xpert HCV VL Fingerstick (Xpert FS) precludes such requirements where specimen collected by simple fingerstick can be loaded directly into the test cartridge with results available within 60 min. The present study compared the performance of this assay for HCV RNA quantitation using both capillary whole blood (CWB) and venous whole blood (VWB) with plasma HCV RNA performed on Abbott Real Time HCV PCR. CWB via fingerstick and VWB via venipuncture collected from serologically confirmed HCV-infected participants were loaded into Xpert HCV VL WB for viral load estimation. Simultaneously Abbott Real Time HCV PCR assay was also performed using plasma (reference method). Among the enrolled participants (n=157), the mean age was 46.22±14.79 years and 63 % were male. HCV RNA was detected in 100 cases (63.7 %), median 5.69 (IQR: 5.00-6.32)log10IU ml-1 on the reference method. Xpert FS showed 100 % sensitivity and specificity using both CWB and VWB. The median viral loads detected in CWB and VWB were 5.52 (IQR: 4.59-6.15) and 5.48 (IQR: 4.61-6.07)log10IU ml-1, respectively. Xpert FS offers potential as true POC enabling accurate diagnosis in a single patient visit to the health-care facility, hence may reduce the number of dropouts with a confirmed diagnosis. However, further real-time studies with larger sample size are warranted.
Collapse
Affiliation(s)
- Reshu Agarwal
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi-110070, India
| | - Ekta Gupta
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi-110070, India
| | - Guresh Kumar
- Department of Biostatistics, Institute of Liver and Biliary Sciences, New Delhi-110070, India
| | - Keshaw Kumar Singh
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi-110070, India
| | - Manoj Kumar Sharma
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi-110070, India
| |
Collapse
|
12
|
Rahimi P, Sharafi H, Bahramali G, SajadianFard F, Asadi NS, Alavian SM, Iranpur Mobarakeh V, Moravej SZ. Prevalence of Naturally-Occurring NS5A and NS5B Resistance-Associated Substitutions in Iranian Patients With Chronic Hepatitis C Infection. Front Microbiol 2021; 11:617375. [PMID: 33584581 PMCID: PMC7876467 DOI: 10.3389/fmicb.2020.617375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Hepatitis C virus (HCV), non-structural 5A (NS5A), and non-structural 5B (NS5B) resistance-associated substitutions (RASs) are the main causes of failure to direct-acting antiviral agents (DAAs). NS5A and NS5B RASs can occur in patients with HCV infection naturally and before exposure to DAAs. OBJECTIVES This study aimed to evaluate naturally-occurring NS5A and NS5B RASs in Iranian patients with HCV genotype 1a (HCV-1a) and -3a infections. METHODS In this cross-sectional study, viral RNA was extracted from serum specimens. NS5A and NS5B regions were amplified using RT-PCR followed by DNA sequencing. The results of nucleotide sequences were aligned against reference sequences of HCV-1a and -3a and the amino acid substitutions were analyzed using geno2pheno [hcv] web application. RESULTS Among 135 patients with hepatitis C, NS5A amino acid substitutions/RASs were identified in 26.4% and 15.9% of patients with HCV-1a and -3a infections, respectively. The identified amino acid substitutions/RASs in the NS5A region of patients with HCV-1a infection were M28T/V/I 11.1%, Q30R/H 4.2%, L31M 1.4%, and H58Y/P/C/D/Q/S/T 16.7%. Y93H substitution was not found in HCV-1a sequences. In patients with HCV-3a infection, NS5A amino acid substitutions/RASs were A30T/K 9.5%, L31F 1.6%, P58S/T/C 3.2%, Y93H 3.2%, and Y93N 3.2%. No resistance substitutions were identified in NS5B sequences from patients with HCV-1a and -3a infections. CONCLUSION In this study, baseline amino acid substitutions/RASs were only identified in the NS5A region in Iranian patients with HCV-1a and -3a infections, and the prevalence of these amino acid substitutions/RASs were in accordance with similar studies. There were no RASs in the HCV-1a and -3a NS5B region.
Collapse
Affiliation(s)
- Pooneh Rahimi
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | | | - Golnaz Bahramali
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | | | | | | | | | | |
Collapse
|
13
|
Isfordink CJ, van de Laar TJW, Rebers SPH, Wessels E, Molenkamp R, Knoester M, Baak BC, van Nieuwkoop C, van Hoek B, Brakenhoff SM, Blokzijl H, Arends JE, van der Valk M, Schinkel J. Direct-Acting Antiviral Treatment for Hepatitis C Genotypes Uncommon in High-Income Countries: A Dutch Nationwide Cohort Study. Open Forum Infect Dis 2021; 8:ofab006. [PMID: 33614815 PMCID: PMC7881754 DOI: 10.1093/ofid/ofab006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Background The majority of hepatitis C virus (HCV) infections are found in low- and middle-income countries, which harbor many region-specific HCV subtypes. Nevertheless, direct-acting antiviral (DAA) trials have almost exclusively been conducted in high-income countries, where mainly epidemically spread HCV subtypes are present. Recently, several studies have demonstrated suboptimal DAA efficacy for certain nonepidemic subtypes, which could hamper global HCV elimination. Therefore, we aimed to evaluate DAA efficacy in patients treated for a nonepidemic HCV genotype infection in the Netherlands. Methods We performed a nationwide retrospective study including patients treated with interferon-free DAAs for an HCV genotype other than 1a/1b/2a/2b/3a/4a/4d. The genotype was determined by NS5B region phylogenetic analysis. The primary end point was SVR-12. If stored samples were available, NS5A and NS5B sequences were obtained for resistance-associated substitutions (RAS) evaluation. Results We included 160 patients, mainly infected with nonepidemic genotype 2 (41%) and 4 (31%) subtypes. Most patients were from Africa (45%) or South America (24%); 51 (32%) were cirrhotic. SVR-12 was achieved in 92% (140/152) of patients with available SVR-12 data. Only 73% (8/11) genotype 3–infected patients achieved SVR-12, the majority being genotype 3b patients with 63% (5/8) SVR. Regardless of SVR, all genotype 3b patients had 30K and 31M RAS. Conclusions The DAA efficacy we observed in most nonepidemic genotypes in the Netherlands seems reassuring. However, the low SVR-12 rate in subtype 3b infections is alarming, especially as it is common in several HCV-endemic countries. Alongside earlier results, our results indicate that a remaining challenge for global HCV elimination is confirming and monitoring DAA efficacy in nonepidemic genotypes.
Collapse
Affiliation(s)
- Cas J Isfordink
- Department of Infectious Diseases, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Department of Gastroenterology and Hepatology, UMC Utrecht, Utrecht, the Netherlands
| | - Thijs J W van de Laar
- Department of Donor Medicine Research, Laboratory of Blood-borne infections, Sanquin Research, Sanquin Diagnostic Services, Amsterdam, the Netherlands.,Laboratory of Medical Microbiology, Onze Lieve Vrouwe Gasthuis, Amsterdam, the Netherlands
| | - Sjoerd P H Rebers
- Department of Medical Microbiology, Section of Clinical Virology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Els Wessels
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Marjolein Knoester
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bert C Baak
- Department of Gastroenterology and Hepatology, Onze Lieve Vrouwe Gasthuis locatie Oost, Amsterdam, the Netherlands
| | - Cees van Nieuwkoop
- Department of Internal Medicine, Haga Teaching Hospital, The Hague, the Netherlands
| | - Bart van Hoek
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sylvia M Brakenhoff
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Hans Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Joop E Arends
- Department of Internal Medicine and Infectious Diseases, UMC Utrecht, Utrecht, the Netherlands
| | - Marc van der Valk
- Department of Infectious Diseases, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology, Section of Clinical Virology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
14
|
Focus on hepatitis C virus genotype distribution in Tunisia prior to elimination: a 16-year retrospective study. Arch Virol 2021; 166:501-510. [PMID: 33394169 DOI: 10.1007/s00705-020-04918-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/30/2020] [Indexed: 12/12/2022]
Abstract
With the introduction of direct-acting antiviral treatment (DAA), Tunisia has committed to achieving the international goal of eliminating viral hepatitis. Because the specific DAA prescribed depends on viral genotype, viral genotyping remains of great importance. The aim of the present study was to outline the trends in the distribution of HCV genotypes from 2002 to 2017 in the Tunisian general population in order to guide authorities towards the most appropriate therapeutic strategies for preventing HCV infection. A total of 2532 blood samples were collected over a 16-year period and from all regions of Tunisia. Genotyping showed that genotype 1 (subtype 1b) was the most prevalent genotype in the country (n = 2012; 79.5%), followed by genotype 2 (n = 339; 13.3%). Genotypes 3, 4 and 5 were detected in 4.8%, 2.2% and 0.1% of the country's population, respectively. Mixed infections with different HCV genotypes were detected in 0.1% of the population (one case each of genotypes 1b + 4, 1b + 2 and 2 + 4). Interestingly, a significant increase in genotypes 2, 3 and 4 was observed over time (p = 0.03). Sixteen different subtypes were detected over the study period, most of which were subtypes of genotype 2, and some of these subtypes appeared to be new. Patients infected with genotypes 1a, 3 and 4 were significantly younger than those infected with genotypes 1b and 2 (p < 0.01). Furthermore, genotypes 1b and 2 were detected more often in women than men, while genotypes 1a and 3 were detected mostly in men (P < 0.01). Our study confirms a large predominance of genotype1/subtype1b in Tunisia and shows a significant increase in the prevalence of other genotypes over time. These findings reinforce the need for an additional HCV genotype survey to improve the design of treatment strategies in Tunisia.
Collapse
|
15
|
Fourati S, Rodriguez C, Soulier A, Donati F, Hamadat S, Poiteau L, Demontant V, Brillet R, Ahnou N, Gricourt G, Chevaliez S, Ahmed-Belkacem A, Pawlotsky JM. Fitness-associated substitutions following failure of direct-acting antivirals assessed by deep sequencing of full-length hepatitis C virus genomes. Aliment Pharmacol Ther 2020; 52:1583-1591. [PMID: 32886807 DOI: 10.1111/apt.16054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/20/2020] [Accepted: 08/02/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND In hepatitis C virus (HCV) infection, treatment failure is generally associated with the selection of resistance-associated substitutions (RAS) conferring reduced susceptibility to direct-acting antiviral (DAA) drugs. Resistant variants continue to replicate after the end of treatment with potential for transmission. This may result from the selection of "fitness-associated substitutions". AIM To characterise potential "fitness-associated substitutions" in patients infected with genotype 3a failing DAA drugs METHODS: By means of shotgun metagenomics, we sequenced full-length HCV genomes at treatment initiation and at virological relapse in eight patients infected with genotype 3a with cirrhosis failing sofosbuvir and an NS5A inhibitor. The impact of amino acid changes occurring outside of DAA target regions selected in at least two patients were assessed on the in vitro susceptibility to an NS5A inhibitor and replication capacity. RESULTS At treatment failure, besides selection of known NS5A RASs, especially Y93H, a large number of amino acid changes was observed outside of DAA target regions. We identified four amino acid positions at which observed changes substantially improved in vitro replication capacity without affecting NS5A inhibitor susceptibility. CONCLUSIONS This is the first in vivo observation combined with in vitro confirmation of selection of phenotypically characterised "fitness-associated substitutions" together with RASs at the time of sofosbuvir-NS5A inhibitor treatment failure in patients infected with genotype 3a with cirrhosis. Our findings may explain the persistence of resistant HCV variants after treatment in patients who did not achieve sustained virological remission.
Collapse
Affiliation(s)
- Slim Fourati
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Christophe Rodriguez
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Alexandre Soulier
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Flora Donati
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Sabah Hamadat
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Lila Poiteau
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | | | | | - Nazim Ahnou
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | | | - Stéphane Chevaliez
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Abdelhakim Ahmed-Belkacem
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Jean-Michel Pawlotsky
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| |
Collapse
|
16
|
Substitution of the CD81 Binding Site and β-Sandwich Area in E2 of HCV in Cambodia. Viruses 2020; 12:v12050551. [PMID: 32429467 PMCID: PMC7290788 DOI: 10.3390/v12050551] [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: 05/09/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
The high genetic variability of hepatitis C virus (HCV) is the main obstacle to developing a vaccine. E2 has attracted attention for vaccine development because targeting this protein could potentially overcome issues related to the genetic diversity of HCV. In this study, we analyzed HCV genes in the general population of Cambodia and investigated the E2 locus as a candidate for vaccine development. HCV sero-epidemiological surveys were conducted between the period 2010 and 2014, with an HCV RNA–positive rate of 1.3% (11/868). Follow-up blood samples were collected from four anti-HCV– and HCV RNA– positive patients (genotype 1b: 2 cases, 6e: 1 case, 6r: 1 case) after 4.12 years. Analysis of HCV full-length nucleotide sequences in paired specimens revealed that the mutation rates of HCV genotypes 1b and 6e/6r were 1.61–2.03 × 10−3 and 2.52–2.74 × 10−3 substitutions/site/year, respectively. Non-synonymous substitutions were detected in HVR1, the front layer of the CD81 binding site, and the β-sandwich, but not in the N-terminal region or adjacent to the CD81 binding site. Therefore, we conclude that the CD81 binding site is a promising locus for HCV vaccine development.
Collapse
|
17
|
New Diagnostic Approaches to Viral Sexually Transmitted Infections. Sex Transm Infect 2020. [DOI: 10.1007/978-3-030-02200-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
18
|
Larouche A, Milton McSween KA, Calderon V, Fauteux-Daniel S, Boulais J, Ransy DG, Boucher M, Lamarre V, Lapointe N, Boucoiran I, Money DM, Krajden M, Le Campion A, Soudeyns H. Quasispecies Diversity Is a Major Risk Factor for Vertical Hepatitis C Virus Transmission. J Infect Dis 2019; 219:760-771. [PMID: 30365007 DOI: 10.1093/infdis/jiy581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/11/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Vertical transmission is the major cause of pediatric hepatitis C virus (HCV) infection. The objective of this study was to better understand HCV pathogenesis in pregnant women and provide insights into risk factors and mechanisms involved in vertical transmission. METHODS Evolutionary dynamics of HCV variant spectra and HCV-specific neutralizing antibody responses were examined using high-throughput sequencing and pseudoparticle-based assays in pregnant women monoinfected with HCV (n = 17) or coinfected with HCV and human immunodeficiency virus (HIV)-1 (n = 15). RESULTS Overall, statistically significant associations were found between HCV quasispecies diversity, selective pressure exerted on the HCV E2 envelope protein, and neutralizing activity of maternal immunoglobulins. Women with low quasispecies diversity displayed significantly higher mean aspartate aminotransferase and alanine aminotransferase levels throughout pregnancy, but this difference was restricted to monoinfected participants. Low quasispecies diversity and inefficient neutralizing activity were also significantly associated with vertical transmission, but only in the monoinfected group. CONCLUSIONS These results indicate that maternal neutralizing antibody responses play a role in the prevention of vertical HCV transmission, but not in presence of HIV-1 coinfection, and suggest that the mechanism of vertical transmission may be different between monoinfected and coinfected women. These findings could inform management strategies for the prevention of vertical HCV transmission.
Collapse
Affiliation(s)
- Ariane Larouche
- Unité immunopathologie virale, Centre de recherche du Centre hospitalier universitaire (CHU) Sainte-Justine, Montreal, Quebec, Canada.,Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Canada
| | - Kimberly-Ann Milton McSween
- Unité immunopathologie virale, Centre de recherche du Centre hospitalier universitaire (CHU) Sainte-Justine, Montreal, Quebec, Canada.,Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Canada
| | - Virginie Calderon
- Unité immunopathologie virale, Centre de recherche du Centre hospitalier universitaire (CHU) Sainte-Justine, Montreal, Quebec, Canada.,Department of Informatics and Operations Research, Université de Montréal, Canada
| | - Sébastien Fauteux-Daniel
- Unité immunopathologie virale, Centre de recherche du Centre hospitalier universitaire (CHU) Sainte-Justine, Montreal, Quebec, Canada.,Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Canada
| | - Jonathan Boulais
- Centre de recherche du CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Doris G Ransy
- Unité immunopathologie virale, Centre de recherche du Centre hospitalier universitaire (CHU) Sainte-Justine, Montreal, Quebec, Canada.,Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Canada
| | - Marc Boucher
- Centre maternel et infatile sur le SIDA, Centre de recherche du CHU Sainte-Justine, Montreal, Quebec.,Departement of Obstetrics and Gynecology, Faculty of Medicine, Université de Montréal, Canada
| | - Valérie Lamarre
- Centre maternel et infatile sur le SIDA, Centre de recherche du CHU Sainte-Justine, Montreal, Quebec.,Department of Pediatrics, Faculty of Medicine, Université de Montréal, Canada
| | - Normand Lapointe
- Centre maternel et infatile sur le SIDA, Centre de recherche du CHU Sainte-Justine, Montreal, Quebec.,Department of Pediatrics, Faculty of Medicine, Université de Montréal, Canada
| | - Isabelle Boucoiran
- Centre maternel et infatile sur le SIDA, Centre de recherche du CHU Sainte-Justine, Montreal, Quebec.,Departement of Obstetrics and Gynecology, Faculty of Medicine, Université de Montréal, Canada
| | | | - Mel Krajden
- BC Center for Disease Control, Vancouver, Canada
| | - Armelle Le Campion
- Unité immunopathologie virale, Centre de recherche du Centre hospitalier universitaire (CHU) Sainte-Justine, Montreal, Quebec, Canada.,Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Canada
| | - Hugo Soudeyns
- Unité immunopathologie virale, Centre de recherche du Centre hospitalier universitaire (CHU) Sainte-Justine, Montreal, Quebec, Canada.,Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Canada.,Department of Pediatrics, Faculty of Medicine, Université de Montréal, Canada
| |
Collapse
|
19
|
Parr JB, Lodge EK, Holzmayer V, Pepin J, Frost EH, Fried MW, McGivern DR, Lemon SM, Keeler C, Emch M, Mwandagalirwa K, Tshefu A, Fwamba F, Muwonga J, Meshnick SR, Cloherty G. An Efficient, Large-Scale Survey of Hepatitis C Viremia in the Democratic Republic of the Congo Using Dried Blood Spots. Clin Infect Dis 2019; 66:254-260. [PMID: 29048459 DOI: 10.1093/cid/cix771] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/24/2017] [Indexed: 02/07/2023] Open
Abstract
Background Efficient viral load testing is needed for hepatitis C (HCV) surveillance and diagnosis. HCV viral load testing using dried blood spots (DBSs), made with a single drop of finger-prick whole blood on filter paper, is a promising alternative to traditional serum- or plasma-based approaches. Methods We adapted the Abbott Molecular m2000 instrument for high-throughput HCV viremia testing using DBSs with simple specimen processing and applied these methods to estimate the national burden of infection in the Democratic Republic of the Congo (DRC). We tested DBSs collected during the 2013-2014 DRC Demographic and Health Survey, including 1309 adults ≥40 years of age. HCV-positive samples underwent targeted sequencing, genotyping, and phylogenetic analyses. Results This high-throughput screening approach reliably identified HCV RNA extracted from DBSs prepared using whole blood, with a 95% limit of detection of 1196 (95% confidence interval [CI], 866-2280) IU/mL for individual 6-mm punches and 494 (95% CI, 372-1228) IU/mL for larger 12-mm punches. Fifteen infections were identified among samples from the DRC Demographic and Health Survey; the weighted country-wide prevalence of HCV viremia was 0.9% (95% CI, 0.3%-1.6%) among adults ≥40 years of age and 0.7% (95% CI, .6%-.8%) among human immunodeficiency virus-infected subjects. All successfully genotyped cases were due to genotype 4 infection. Conclusions DBS-based HCV testing represents a useful tool for the diagnosis and surveillance of HCV viremia and can easily be incorporated into specimen referral systems. Among adults ≥40 years of age in the DRC, 100000-200000 may have active infection and be eligible for treatment.
Collapse
Affiliation(s)
- Jonathan B Parr
- Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill
| | - Evans K Lodge
- School of Medicine, University of North Carolina, Chapel Hill
| | | | | | | | - Michael W Fried
- Division of Gastroenterology, Department of Medicine, University of North Carolina, Chapel Hill
| | - David R McGivern
- Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill
| | - Stanley M Lemon
- Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill
| | - Corinna Keeler
- Department of Geography, University of North Carolina, Chapel Hill
| | - Michael Emch
- Department of Geography, University of North Carolina, Chapel Hill.,Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina, Chapel Hill
| | - Kashamuka Mwandagalirwa
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina, Chapel Hill.,Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | - Antoinette Tshefu
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | - Franck Fwamba
- National AIDS Control Program, Kinshasa, Democratic Republic of Congo
| | - Jérémie Muwonga
- National AIDS Control Program, Kinshasa, Democratic Republic of Congo
| | - Steven R Meshnick
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina, Chapel Hill
| | | |
Collapse
|
20
|
Molecular surveillance of hepatitis C virus genotypes identifies the emergence of a genotype 4d lineage among men in Quebec, 2001-2017. ACTA ACUST UNITED AC 2019; 45:230-237. [PMID: 31650986 DOI: 10.14745/ccdr.v45i09a02] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Background Molecular phylogenetics are generally used to confirm hepatitis C virus (HCV) transmission events. In addition, the Laboratoire de santé publique du Québec (LSPQ) has been using molecular phylogenetics for surveillance of HCV genotyping since November 2001. Objectives To describe the emergence of a specific lineage of HCV genotype 4d (G4d) and its characteristics using molecular phylogenetics as a surveillance tool for identifying HCV strain clustering. Methods The LSPQ prospectively applied Sanger sequencing and phylogenetic analysis to determine the HCV genotype on samples collected from November 2001 to December 2017. When a major G4d cluster was identified, demographic information, HIV-infection status and syphilis test results were analyzed. Results Phylogenetic analyses performed on approximately 22,000 cases identified 122 G4d cases. One major G4d cluster composed of 37 cases was singled out. Two cases were identified in 2010, 10 from 2011-2014 and 25 from 2015-2017. Cases in the cluster were concentrated in two urban health regions. Compared to the other G4d cases, cluster cases were all male (p<0.001) and more likely to be HIV-positive (adjusted risk ratio: 4.4; 95% confidence interval: 2.5-7.9). A positive syphilis test result was observed for 27 (73%) of the cluster cases. The sequences in this cluster and of four outlier cases were located on the same monophyletic lineage as G4d sequences reported in HIV-positive men who have sex with men (MSM) in Europe. Conclusion Molecular phylogenetics enabled the identification and surveillance of ongoing transmission of a specific HCV G4d lineage in HIV-positive and HIV-negative men in Quebec and its cross-continental spread. This information can orient intervention strategies to avoid transmission of HCV in MSM.
Collapse
|
21
|
High prevalence of genotype 6 hepatitis C virus infection in Southern Taiwan using Abbott genotype assays. J Formos Med Assoc 2019; 119:413-419. [PMID: 31420113 DOI: 10.1016/j.jfma.2019.07.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/12/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND/PURPOSE Abbott RealTime Genotype II assay can effectively identify hepatitis C virus (HCV) genotypes (GTs), but some GT 6 subtypes might not be differentiated from GT 1. Abbott RealTime Genotype II PLUS and sequencing might be needed to resolve these ambiguous results. Unlike the high prevalence of GT 6 in Southeast Asia, GT 6 had rarely been reported in Taiwan except in intravenous drug abusers (IDU). But the prevalence of GT 6 in Taiwan might be underestimated. We conducted this study to determine the GTs in a HCV endemic area in Southern Taiwan. METHODS A total of 1147 patients with hepatitis C viremia for direct acting antivirals (DAA) treatment at the Chi Mei medical system in Tainan were enrolled. Genotype was determined using a working flow consisted of Abbott GT II, PLUS assays and 5' untranslated region (5' UTR)/core sequencing. RESULTS Among the 1147 patients, 883 (77.0%) obtained GT results by GT II, 264 (23.0%) samples with ambiguous results by GT II assay received further tests, including 194 (73.5%) with PLUS assay and 70 (26.5%) with 5'UTR/core sequencing. Nearly three-quarters (73.5%) of ambiguous results by GT II assay were GT 6. Overall, 18.3% of samples were GT 6. Phylogenetic study of 11 samples of GT 6 subtypes showed 7 (63.6%) were 6 g. CONCLUSION GT 6 is the major factor for high ambiguous rate by GT II. Unexpected high prevalence of GT 6 (18.3%) in Southern Taiwan, especially subtype 6 g, closely related to Indonesian strains, is first reported.
Collapse
|
22
|
Tagnouokam-Ngoupo PA, Ngoufack MN, Kenmoe S, Lissock SF, Amougou-Atsama M, Banai R, Ngono L, Njouom R. Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients. Virol J 2019; 16:101. [PMID: 31399103 PMCID: PMC6688274 DOI: 10.1186/s12985-019-1214-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/06/2019] [Indexed: 12/23/2022] Open
Abstract
Background Current HCV treatments are genotype specific although potential pan-genotype treatments have recently been described. Therefore, genotyping is an essential tool for the therapeutic management of HCV infection and a variety of technologies have been developed for HCV genotypes determination. Sequences analysis of HCV sub-genomic regions is considered as gold standard and is widely used for HCV genotyping. Here, we compared HCV genotyping using core and NS5B regions in routine practice in HCV-positive Cameroonian patients. Methods All plasma samples received at Centre Pasteur of Cameroon (CPC) in 2016 for HCV genotyping were included. Viral loads were determined using the Abbott Real Time assay. Further, genotyping was based on the amplification and sequencing of core and NS5B regions following by phylogenetic analysis of corresponding sequences. Results A total of 369 samples were received during the study period with high viral load values (median: 930,952 IU/ml; IQR: 281,833-2,861,179). Positive amplification was obtained in at least one genomic region (core or NS5B) for all the samples with similar amplification rate in the two genomic regions (p = 0.34). Phylogenetic analysis showed that among the 369 samples, 146 (39.6%) were classified as genotype 4, 132 (35.8%) as genotype 1, 89 (24.1%) as genotype 2, in both core and NS5B regions. Interestingly, for two samples (0.54%) discordant genotypes were obtained in both regions with the core region classified as genotype 4 while the NS5B was identified as genotype 1 indicating the presence of putative HCV recombinant virus or multiple infections in these samples. Discrimination of HCV subtypes was most likely possible with NS5B compared to core region. Conclusions We found high amplification rates of HCV in both core and NS5B regions, and a good concordance was obtained at genotype level using both regions except for two samples where putative 1–4 recombinants/multiple infections were detected. Therefore, HCV genotyping based on at least two genomic regions could help to identify putative recombinants and improve therapeutic management of HCV infection.
Collapse
Affiliation(s)
| | - Marie Nicole Ngoufack
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Sebastien Kenmoe
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Simon Frédéric Lissock
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Marie Amougou-Atsama
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Robert Banai
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Laure Ngono
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon
| | - Richard Njouom
- Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon.
| |
Collapse
|
23
|
Merat SJ, Bru C, van de Berg D, Molenkamp R, Tarr AW, Koekkoek S, Kootstra NA, Prins M, Ball JK, Bakker AQ, de Jong MD, Spits H, Beaumont T, Schinkel J. Cross-genotype AR3-specific neutralizing antibodies confer long-term protection in injecting drug users after HCV clearance. J Hepatol 2019; 71:14-24. [PMID: 30797052 DOI: 10.1016/j.jhep.2019.02.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 01/29/2019] [Accepted: 02/12/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIMS In order to design an effective vaccine against hepatitis C virus (HCV) infection, it is necessary to understand immune protection. A number of broadly reactive neutralizing antibodies have been isolated from B cells of HCV-infected patients. However, it remains unclear whether B cells producing such antibodies contribute to HCV clearance and long-term immune protection against HCV. METHODS We analysed the B cell repertoire of 13 injecting drug users from the Amsterdam Cohort Study, who were followed up for a median of 17.5 years after primary infection. Individuals were classified into 2 groups based on the outcome of HCV infection: 5 who became chronically infected either after primary infection or after reinfection, and 8 who were HCV RNA negative following spontaneous clearance of ≥1 HCV infection(s). From each individual, 10,000 CD27+IgG+B cells, collected 0.75 year after HCV infection, were cultured to characterize the antibody repertoire. RESULTS Using a multiplex flow cytometry-based assay to study the antibody binding to E1E2 from genotype 1 to 6, we found that a high frequency of cross-genotype antibodies was associated with spontaneous clearance of 1 or multiple infections (p = 0.03). Epitope specificity of these cross-genotype antibodies was determined by alanine mutant scanning in 4 individuals who were HCV RNA negative following spontaneous clearance of 1 or multiple infections. Interestingly, the cross-genotype antibodies were mainly antigenic region 3 (AR3)-specific and showed cross-neutralizing activity against HCV. In addition to AR3 antibodies, 3 individuals developed antibodies recognizing antigenic region 4, of which 1 monoclonal antibody showed cross-neutralizing capacity. CONCLUSIONS Together, these data suggest that a strong B cell response producing cross-genotype and neutralizing antibodies, especially targeting AR3, contributes to HCV clearance and long-term immune protection against HCV. LAY SUMMARY Although effective treatments against hepatitis C virus (HCV) are available, 500,000 people die from liver disease caused by HCV each year and approximately 1.75 million people are newly infected. This could be prevented by a vaccine. To design a vaccine against HCV, more insight into the role of antibodies in the protection against HCV infection is needed. In a cohort of injecting drug users, we found that antibodies interfering with virus cell entry, and recognizing multiple HCV genotypes, conferred long-term protection against chronic HCV infection.
Collapse
Affiliation(s)
| | - Camille Bru
- AIMM Therapeutics, Amsterdam, the Netherlands
| | | | - Richard Molenkamp
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Alexander W Tarr
- School of Life Sciences, The University of Nottingham, Nottingham, UK; NIHR Nottingham BRC, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Sylvie Koekkoek
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Maria Prins
- Public Health Service of Amsterdam, Amsterdam, the Netherlands; Department of Infectious Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Jonathan K Ball
- School of Life Sciences, The University of Nottingham, Nottingham, UK; NIHR Nottingham BRC, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | | | - Menno D de Jong
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | | | | | - Janke Schinkel
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
| |
Collapse
|
24
|
Hayashi K, Tachi K, Shimizu Y, Nagano K, Ishizu Y, Kuzuya T, Honda T, Ishigami M, Hirooka Y, Hattori M, Goto H. The Prevalence of Mixed Hepatitis C Virus Genotype Infection and Its Effect on the Response to Direct-Acting Antivirals Therapy. Intervirology 2019; 62:23-29. [PMID: 31207601 DOI: 10.1159/000499691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/15/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The incidence of mixed hepatitis C virus (HCV) genotype infection is variable, and a few reports exist regarding the efficacy of direct-acting antivirals (DAA) therapy for mixed genotype. We aimed to investigate the prevalence of mixed genotype and its impact on the virologic response to DAA therapy. METHODS A total of 365 patients with chronic HCV infection who completed antiviral therapy were recruited. Nested polymerase chain reaction with universal and specific primers of genotypes 1b and 2 and direct sequencing were used for HCV genotyping. RESULTS Direct sequencing with universal primers defined genotypes 1b (n = 230), 2a (n = 95), and 2b (n = 40). Direct sequencing of genotype 2 was performed in patients with genotype 1b, and direct sequencing of genotype 1b in patients with genotype 2. Four patients with genotype 1b underwent amplification for genotype 2, and direct sequencing identified genotypes 1b (n = 1), 2a (n = 1), and 2b (n = 2). None with genotype 2 underwent amplification for genotype 1b. Three cases were confirmed to have mixed genotype. CONCLUSIONS Mixed genotype was rare, and hence the impact of mixed genotype on treatment outcome with DAA therapy is expected to be minimal.
Collapse
Affiliation(s)
- Kazuhiko Hayashi
- Department of Gastroenterology and Hepatology, Federation of National Public Service Personnel Mutual Aid Associations Meijo Hospital, Nagoya, Japan, .,Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan,
| | - Kosuke Tachi
- Department of Gastroenterology and Hepatology, Federation of National Public Service Personnel Mutual Aid Associations Meijo Hospital, Nagoya, Japan
| | - Yuko Shimizu
- Department of Gastroenterology and Hepatology, Federation of National Public Service Personnel Mutual Aid Associations Meijo Hospital, Nagoya, Japan
| | - Kenichi Nagano
- Department of Gastroenterology and Hepatology, Federation of National Public Service Personnel Mutual Aid Associations Meijo Hospital, Nagoya, Japan
| | - Yoji Ishizu
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Teiji Kuzuya
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Honda
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masatoshi Ishigami
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiki Hirooka
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masashi Hattori
- Department of Gastroenterology, Yamashita Hospital, Ichinomiya, Japan
| | - Hidemi Goto
- Department of Gastroenterology and Hepatology, Federation of National Public Service Personnel Mutual Aid Associations Meijo Hospital, Nagoya, Japan.,Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|
25
|
Bettaieb J, Chouikha A, Khedhiri M, Kharroubi G, Badreddine M, Bel Hadj Hmida N, Gharbi A, Hammemi W, Sadraoui A, Ben Yahia A, Meddeb Z, Ben Salah A, Triki H. Hepatitis C virus epidemiology in Central-West Tunisia: a population-based cross-sectional study. Arch Virol 2019; 164:2243-2253. [PMID: 31179516 DOI: 10.1007/s00705-019-04308-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/09/2019] [Indexed: 12/18/2022]
Abstract
This study aimed to assess the seroprevalence, viraemia and genotype distribution of hepatitis C virus (HCV) in a region in Central-West Tunisia. A door-to-door cross-sectional study was conducted on a randomly selected sample. A total of 3178 individuals aged 5 to 74 years and members of 935 families were investigated. Seroprevalence of HCV was assessed using ELISA tests. The viral load was determined by real-time RT-PCR, and HCV genotyping was conducted by amplification and sequencing in the NS5b genomic region. The global prevalence of HCV antibodies was 3.32% (95% confidence interval [CI]: 2.72-4.00). It was significantly higher in women: 4.47% vs. 2.16% in men, p = 0.001. Seroprevalence increased with age, and the highest rates were found in the 50- to 59-year-old age group (12.90%, 95% CI: 9.45-16.86), suggesting a cohort effect with very low contribution of intrafamilial transmission. Genotyping showed a predominance of subtype 1b (84.6%), with cocirculation of subtypes 2c (9.6%), 1a (1.9%), 1d (1.9%) and 2k (1.9%), similar to the previously reported genotype distribution in Tunisia and with no genetic clusters specific to the study region. These results indicate a higher endemicity of HCV infection when compared to the previously reported nationwide surveillance data. This study provides valuable data that can contribute to current strategies to eliminate hepatitis C.
Collapse
Affiliation(s)
- Jihene Bettaieb
- Department of Medical Epidemiology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory: "Transmission, Controle et Immunobiologie des Infections" (LR11-IPT02), Tunis, Tunisia.,Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Faculty of Medicine of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Anissa Chouikha
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, 13 Place Pasteur BP-74, 1002, Tunis Belvedere, Tunisia. .,Research Laboratory: "Transmission, Controle et Immunobiologie des Infections" (LR11-IPT02), Tunis, Tunisia. .,Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.
| | - Marwa Khedhiri
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, 13 Place Pasteur BP-74, 1002, Tunis Belvedere, Tunisia.,Research Laboratory: "Transmission, Controle et Immunobiologie des Infections" (LR11-IPT02), Tunis, Tunisia.,Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Ghassen Kharroubi
- Department of Medical Epidemiology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory: "Transmission, Controle et Immunobiologie des Infections" (LR11-IPT02), Tunis, Tunisia.,Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Faculty of Medicine of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Malek Badreddine
- Department of Medical Epidemiology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Faculty of Medicine of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Nabil Bel Hadj Hmida
- Department of Medical Epidemiology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory: "Transmission, Controle et Immunobiologie des Infections" (LR11-IPT02), Tunis, Tunisia.,Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Adel Gharbi
- Department of Medical Epidemiology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory: "Transmission, Controle et Immunobiologie des Infections" (LR11-IPT02), Tunis, Tunisia.,Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Walid Hammemi
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, 13 Place Pasteur BP-74, 1002, Tunis Belvedere, Tunisia.,Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Amel Sadraoui
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, 13 Place Pasteur BP-74, 1002, Tunis Belvedere, Tunisia.,Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Ahlem Ben Yahia
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, 13 Place Pasteur BP-74, 1002, Tunis Belvedere, Tunisia.,Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Zina Meddeb
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, 13 Place Pasteur BP-74, 1002, Tunis Belvedere, Tunisia.,Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Afif Ben Salah
- Department of Medical Epidemiology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory: "Transmission, Controle et Immunobiologie des Infections" (LR11-IPT02), Tunis, Tunisia.,Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Faculty of Medicine of Tunis, University Tunis El Manar, Tunis, Tunisia.,Department of Community and Family Medicine, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Henda Triki
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, 13 Place Pasteur BP-74, 1002, Tunis Belvedere, Tunisia.,Research Laboratory: "Transmission, Controle et Immunobiologie des Infections" (LR11-IPT02), Tunis, Tunisia.,Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Faculty of Medicine of Tunis, University Tunis El Manar, Tunis, Tunisia
| |
Collapse
|
26
|
Hahn JA, Tully DC, Evans JL, Morris MD, Briceno A, Bean DJ, Allen TM, Page K. Role of HCV Viremia in Corroborated HCV Transmission Events Within Young Adult Injecting Partnerships. Open Forum Infect Dis 2019; 6:ofz125. [PMID: 31041340 PMCID: PMC6483127 DOI: 10.1093/ofid/ofz125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/05/2019] [Indexed: 12/31/2022] Open
Abstract
Background Hepatitis C virus (HCV), a major cause of morbidity and mortality, is common and rising among young persons who inject drugs (PWID). Reducing the level of viremia may be an intervention, yet the impact of viremia on HCV transmission is unknown. Methods We conducted a prospective study of injecting partnerships (Partner Study) of young adult (age < 30 years) PWID within the UFO Study, which enrolled those at risk for HCV or with seronegative viremic infection and up to 3 HCV RNA-positive regular injecting partners. We examined the level of HCV viremia and stage of infection in the HCV-positive partner in regression analyses of HCV transmission events that were corroborated via HCV phylogenetic linkage analyses. Results We enrolled 69 at-risk/acutely infected PWID. There were 25 new HCV infections (incidence rate, 35.9 per 100 person-years; 95% confidence interval [CI], 24.3-53.2 per 100 person-years); 12/25 (48%) were phylogenetically linked to at least 1 partner. We found no association between the infected partner's quantitative level of HCV viremia and likely transmission in multivariate analyses (adjusted odds ratio [AOR], 0.90; 95% confidence interval [CI], 0.55-1.46); however, seronegative viremic infection in the infected partner was associated with increased transmission (AOR, 28.02; 95% CI, 5.61-139.95). Conclusions The HCV viremia level was not associated with increased odds of transmission, yet acute HCV infection (seronegative viremic) was. Explanations include high-risk behavior during acute infection or missed fluctuations in viremia during acute infection. Both point to the need for frequent testing to detect new infection and attempt to prevent onward transmission.
Collapse
Affiliation(s)
- Judith A Hahn
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Damien C Tully
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jennifer L Evans
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Meghan D Morris
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Alya Briceno
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - David J Bean
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Todd M Allen
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | | |
Collapse
|
27
|
Davis C, Mgomella GS, da Silva Filipe A, Frost EH, Giroux G, Hughes J, Hogan C, Kaleebu P, Asiki G, McLauchlan J, Niebel M, Ocama P, Pomila C, Pybus OG, Pépin J, Simmonds P, Singer JB, Sreenu VB, Wekesa C, Young EH, Murphy DG, Sandhu M, Thomson EC. Highly Diverse Hepatitis C Strains Detected in Sub-Saharan Africa Have Unknown Susceptibility to Direct-Acting Antiviral Treatments. Hepatology 2019; 69:1426-1441. [PMID: 30387174 PMCID: PMC6492010 DOI: 10.1002/hep.30342] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/30/2018] [Indexed: 12/11/2022]
Abstract
The global plan to eradicate hepatitis C virus (HCV) led by the World Health Organization outlines the use of highly effective direct-acting antiviral drugs (DAAs) to achieve elimination by 2030. Identifying individuals with active disease and investigation of the breadth of diversity of the virus in sub-Saharan Africa (SSA) is essential as genotypes in this region (where very few clinical trials have been carried out) are distinct from those found in other parts of the world. We undertook a population-based, nested case-control study in Uganda and obtained additional samples from the Democratic Republic of Congo (DRC) to estimate the prevalence of HCV, assess strategies for disease detection using serological and molecular techniques, and characterize genetic diversity of the virus. Using next-generation and Sanger sequencing, we aimed to identify strains circulating in East and Central Africa. A total of 7,751 Ugandan patients were initially screened for HCV, and 20 PCR-positive samples were obtained for sequencing. Serological assays were found to vary significantly in specificity for HCV. HCV strains detected in Uganda included genotype (g) 4k, g4p, g4q, and g4s and a newly identified unassigned g7 HCV strain. Two additional unassigned g7 strains were identified in patients originating from DRC (one partial and one full open reading frame sequence). These g4 and g7 strains contain nonstructural (ns) protein 3 and 5A polymorphisms associated with resistance to DAAs in other genotypes. Clinical studies are therefore indicated to investigate treatment response in infected patients. Conclusion: Although HCV prevalence and genotypes have been well characterized in patients in well-resourced countries, clinical trials are urgently required in SSA, where highly diverse g4 and g7 strains circulate.
Collapse
Affiliation(s)
- Chris Davis
- Medical Research Council ‐ University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - George S. Mgomella
- Department of Medicine ‐ University of CambridgeCambridgeCambridgeshireUnited Kingdom
- Wellcome Sanger InstituteHinxtonCambridgeshireUnited Kingdom
| | - Ana da Silva Filipe
- Medical Research Council ‐ University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | | | | | - Joseph Hughes
- Medical Research Council ‐ University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | | | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine Uganda Research UnitEntebbeUganda
- Uganda Virus Research InstituteEntebbeUganda
| | | | - John McLauchlan
- Medical Research Council ‐ University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Marc Niebel
- Medical Research Council ‐ University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Ponsiano Ocama
- Department of MedicineMakerere University College of Health SciencesKampalaUganda
| | - Cristina Pomila
- Department of Medicine ‐ University of CambridgeCambridgeCambridgeshireUnited Kingdom
| | - Oliver G. Pybus
- Department of ZoologyUniversity of OxfordOxfordUnited Kingdom
| | | | - Peter Simmonds
- Peter Medawar Building for Pathogen ResearchUniversity of OxfordUnited Kingdom
| | - Joshua B. Singer
- Medical Research Council ‐ University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Vattipally B. Sreenu
- Medical Research Council ‐ University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | | | - Elizabeth H. Young
- Department of Medicine ‐ University of CambridgeCambridgeCambridgeshireUnited Kingdom
- Wellcome Sanger InstituteHinxtonCambridgeshireUnited Kingdom
| | - Donald G. Murphy
- National Institute of Public Health of Quebec, Laboratory of Public Health of QuebecSainte‐Anne‐de‐BellevueQuebecCanada
| | - Manj Sandhu
- Department of Medicine ‐ University of CambridgeCambridgeCambridgeshireUnited Kingdom
- Wellcome Sanger InstituteHinxtonCambridgeshireUnited Kingdom
| | - Emma C. Thomson
- Medical Research Council ‐ University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| |
Collapse
|
28
|
Impact of Preexisting Hepatitis C Virus Genotype 6 NS3, NS5A, and NS5B Polymorphisms on the In Vitro Potency of Direct-Acting Antiviral Agents. Antimicrob Agents Chemother 2019; 63:AAC.02205-18. [PMID: 30718256 DOI: 10.1128/aac.02205-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/29/2019] [Indexed: 12/14/2022] Open
Abstract
HCV genotype 6 (GT-6) is found predominantly in East and Southeast Asia. Clinical studies have focused on patients infected with hepatitis C virus (HCV) GT-6a, where high sustained virologic response (SVR) rates to direct-acting antivirals (DAAs) have been achieved. However, GT-6 is highly diverse, with 29 reported subtypes. We explored the diversity of GT-6 polymorphisms at residues associated with DAA resistance, their impact on DAA in vitro potency when evaluated in a GT-6a consensus replicon, and their association with specific GT-6 subtypes. GT-6 sequences from 25 patient-derived samples and 105 sequences from the U.S. HCV database were compared, and substitutions at resistance-associated residue positions were phenotyped against different DAAs. Preexisting resistance-associated substitutions (RASs) to NS3 protease (A156V and D168E) and NS5B nucleotide (L159F and S282C) inhibitors were rare (<4%). Preexisting RASs to NS5A inhibitors were common, especially at L28 (A/F/G/M/T/V) and R30 (E/N/S). In vitro susceptibilities of NS5A-L28A and -L28T were dramatically reduced against all tested NS5A drugs (90% effective concentration [EC90] range, 119 to 2,032 nM) compared with susceptibilities against a GT-6a consensus replicon (EC90 range, 0.1 to 19 nM). These L28 RASs preexisted in combination with R30S (EC90 [L28A-R30S] of ≥720 nM or EC90 [L28T-R30S] of ≥128 nM against tested DAAs) or as L28T-L31I (EC90 [tested DAAs] of >5,000 nM) and were detected in evaluated GT-6b and -6f sequences. NS5A-L28A-R30A, observed in GT-6r, did not replicate. In conclusion, HCV GT-6b, GT-6f, and GT-6r sequences harbored highly resistant RASs to all evaluated NS5A drugs. Therefore, monitoring SVR in patients infected with these GT-6 subtypes treated with NS5A drug-containing regimens is suggested to confirm any association between noted NS5A polymorphisms and treatment failure.
Collapse
|
29
|
Kao JH, Lin CY, Chuang WL, Cheng YY, Hu JY, Liang WK, Friebe P, Palmer S, Huang CS. Clinical evaluation of IntelliPlex TM HCV genotyping kit for hepatitis C virus genotyping. Diagn Microbiol Infect Dis 2019; 94:344-348. [PMID: 30975461 DOI: 10.1016/j.diagmicrobio.2019.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/12/2019] [Accepted: 02/27/2019] [Indexed: 12/24/2022]
Abstract
Genotyping of the hepatitis C virus (HCV) is crucial for determining the most efficient anti-viral therapy. The clinical sensitivity and specificity of the IntelliPlexTM HCV Genotyping Kit was determined by comparing the assay results of 307 specimens with the results obtained by Sanger sequencing. Out of 202 HCV-positive specimens tested, 8 samples yielded discrepant results between the IntelliPlex HCV Genotyping Kit and Sanger sequencing. For 5 of these discrepant samples, the IntelliPlex HCV Genotyping Kit classified the correct genotype but failed to show the same single or dual infected status as determined by Sanger sequencing. A total of 105 samples which tested negative for HCV by In-Vitro-Diagnostics (IVD)-approved viral load assay tested negative for HCV by the IntelliPlex HCV Genotyping Kit. The IntelliPlex HCV Genotyping Kit has a clinical specificity of 100% and a clinical sensitivity of 96.9% and is suited to be used in clinical laboratories to genotype HCV.
Collapse
Affiliation(s)
- Jia-Horng Kao
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Division of Gastroenterology and Hepatology, the National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Yen Lin
- School of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Wan-Long Chuang
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University, Kaohsiung. Taiwan; Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | | | - Jui-Yu Hu
- PlexBio Co., Ltd., Neihu District, Taipei, Taiwan
| | | | - Peter Friebe
- PlexBio Co., Ltd., Neihu District, Taipei, Taiwan.
| | | | | |
Collapse
|
30
|
Mettikanont P, Bunchorntavakul C, Reddy KR. Systematic review: epidemiology and response to direct-acting antiviral therapy in genotype 6 chronic hepatitis C virus infection. Aliment Pharmacol Ther 2019; 49:492-505. [PMID: 30687952 DOI: 10.1111/apt.15100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/07/2018] [Accepted: 11/27/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Hepatitis C virus (HCV) genotype 6 (GT6) is predominantly encountered in Southeast Asia and data on GT6 response to direct-acting antiviral (DAA) therapy are relatively limited. AIM To review the epidemiology and virologic outcome of DAA regimens in HCV GT6 patients. METHODS Electronic literature search of PubMed, EMBASE, and The Cochrane Library databases were conducted. RESULTS Hepatitis C virus genotype 6 is the most genetically diverse, has a prevalence of 19.9%-95.6% in HCV infected patients in Southeast Asia and has been associated with a higher risk of HCC in those with cirrhosis. After an extensive literature review, a total of 20 studies were selected to assess study population and treatment outcomes (total of 938 GT6 patients were included); 12 were clinical trials and eight were observational studies. Sustained virologic response at week 12 (SVR 12) following glecaprevir/pibrentasvir (n = 4; 108 patients), ledipasvir/sofosbuvir (n = 8; 427 patients), sofosbuvir/velpatasvir with or without voxilaprevir (n = 5; 171 patients), sofosbuvir/daclatasvir (n = 3; 172 patients) and sofosbuvir with ribavirin (n = 3; 60 patients) was 98%-100%, 64%-100%, 100%, 88%-94% and 100%, respectively. Failure was mostly in those with cirrhosis and prior treatment experience. DAA therapy was well tolerated and with a serious adverse event rate of <5%. CONCLUSIONS Hepatitis C virus genotype 6 is genetically diverse and is highly prevalent in Asia. While SVR rates have been high, cirrhosis and prior treatment experience marginally compromise response to DAAs. Large scale and exclusive studies in HCV genotype 6 prevalent areas are needed, while the current evidence suggests that DAAs are highly effective and safe.
Collapse
Affiliation(s)
| | - Chalermrat Bunchorntavakul
- Division of Gastroenterology and Hepatology, Department of Medicine, Rajavithi Hospital, College of Medicine, Rangsit University, Bangkok, Thailand
| | - K Rajender Reddy
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
31
|
Hua R, Jiang X, Qi L, Guan S, Kuai Z, Qiao Y, Xu Y, Gong X, Shi Y, Kong W, Niu J, Zhang H, Shan Y. Screening HCV genotype-specific epitope peptides based on conserved sequence analysis and B cell epitope prediction in HCV E2 region. Immunol Res 2019; 66:67-73. [PMID: 29151181 DOI: 10.1007/s12026-017-8962-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The high mutation rate of the hepatitis C virus (HCV) genome increases the genotype diversity and renders the detection of the virus more difficult. Therefore, prediction and assessment of highly conserved and strongly antigenic epitope polypeptide sequences have become a focus of current research. The E2 region is the target binding region of neutralizing antibodies. HCV genomics, especially the high mutation rate of E2 region sequence, makes its genotyping more and more diverse, and the detection of HCV and genotype is becoming more and more strict. In this study, four HCV B cell epitope polypeptides were constructed based on assessment of conserved sequences in the HCV E2 region and prediction of B cell epitopes, including sequences specific to genotype 1A (DC-13: 434-DTGWLAGLFYYHK-446), genotype 1B (HC-13: 434-HTGFLAALFYAKS-446), genotype 4D (NC-13: 434-NTGFLASLFYTHK-446), and a consensus sequence (FC-9: 447-FNSSGCPER-455). Epitope polypeptides combined with serum from 29 HCV-infected or 25 non-HCV-infected individuals were assayed by enzyme-linked immunosorbent assay (ELISA), and differences were analyzed by T/T' test methods in SPSS v20.0 software. Binding levels of genotype 1A, 4D, and consensus epitope polypeptides with sera of HCV-infected patients were higher than those of non-infected individuals. Moreover, binding of genotype 1B epitope polypeptides with serum of HCV 1B-infected patients was higher than that of HCV 2A-infected patients. While the screening results of HCV genotype-specific epitope polypeptides were preliminary, these findings indicated that we successfully established an HCV and genotype serological ELISA detection method. Such an approach would facilitate the discovery of epitope polypeptides which may become new antigen candidates in peptide vaccine development for the prevention of HCV infection.
Collapse
Affiliation(s)
- Rui Hua
- Department of Hepatology, The First Hospital, Jilin University, Changchun, Jilin, China
| | - Xiaoyu Jiang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Lingxia Qi
- Department of Hepatology, The First Hospital, Jilin University, Changchun, Jilin, China
| | - Shanshan Guan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Ziyu Kuai
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Yongbo Qiao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Yan Xu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Xin Gong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Yuhua Shi
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China.,Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Junqi Niu
- Department of Hepatology, The First Hospital, Jilin University, Changchun, Jilin, China
| | - Hao Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin, China
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China. .,Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin, China.
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Abstract
INTRODUCTION Hepatitis C virus (HCV) is divided into 7 genotypes and 67 subtypes. HCV genotype studies reflect the viral transmission patterns as well as human migration routes. In a clinical setting, HCV genotype is a baseline predictor for the sustained virological response (SVR) in chronic hepatitis C patients treated with peginterferon or some direct acting antivirals (DAAs). The Versant HCV genotype 2.0 assay has been globally used for HCV genotyping over a decade. Areas covered: The assay is based on reverse hybridization principle. It is evolved from its former versions, and the accuracy and successful genotyping/subtyping rate are substantially improved. It shows an accuracy of 99-100% for genotypes 1-6. It can also reliably identify subtypes 1a and 1b. However, the assay does not allow a high resolution for many other subtypes. Reasons for indeterminate or inaccurate genotyping/subtyping results are discussed. Expert commentary: Genotyping helps to find the most efficacious and cost-effective treatment regimen. The rapid development of anti-HCV treatment regimens, however, is greatly simplifying laboratory tests. In the near future, the need for HCV genotyping and frequent serial on-treatment HCV RNA tests will decrease along with the wide use of the more potent and pan-genotypic DAA regimens.
Collapse
Affiliation(s)
- Ruifeng Yang
- a Peking University People's Hospital, Peking University Hepatology Institute , Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases , Beijing , China
| | - Lai Wei
- a Peking University People's Hospital, Peking University Hepatology Institute , Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases , Beijing , China
| |
Collapse
|
34
|
Sagnelli E, Alessio L, Sagnelli C, Gualdieri L, Pisaturo M, Minichini C, Di Caprio G, Starace M, Onorato L, Scotto G, Macera M, Coppola N. Clinical Findings of HCV Chronic Infection in Undocumented Immigrants and Low-Income Refugees in Three Areas of Southern Italy. Ann Hepatol 2018; 17:47-53. [PMID: 29311411 DOI: 10.5604/01.3001.0010.7534] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
INTRODUCTION AND AIM In recent decades, Italy has become a land of immigration from countries suffering a socio-economic crisis. The aim of this study was to perform an organized screening to identify and offer care to immigrants with HCV infection. MATERIAL AND METHODS The screening, performed from 2012 to 2015, involved 1,727 immigrants in the Campania and Apulia regions in southern Italy. RESULTS Screening was accepted by 1,727 (85%) out of 2,032 immigrants interviewed; 70 (4.1%) of the 1,727 were anti-HCV-positive, all unaware of their serological condition, 31 (44.3%) of whom were HCV-RNA-positive and 39 negative. The 31 HCV-RNA-positive immigrants were further investigated at a third-level clinic of infectious diseases. The HCV viral load was 2.6 x 107 ± 7.7 x107 IU/mL, and 35.5% showed HCV-genotype 1a or 1b, 23.8% genotype 2 and 22.6% genotype 3. Two immigrants had liver cirrhosis and, in accordance with the Italian Healthcare Authority guidelines, received an interferon-free regimen and achieved a sustained virological response (SVR); 18 had chronic hepatitis, 6 of whom with a high risk of progression and received interferonbased therapy, with SVR in 4, whereas 12 at low risk were put on a waiting list for future interferon-free treatment, once licensed. The remaining 11 HCV-RNA-positive immigrants were considered HCV inactive chronic carriers and were included in a long-term observational program. CONCLUSION The screening program can be considered successful since it was accepted by 85% of the subjects interviewed and identified 70 anti-HCV-positive immigrants, all unaware of their clinical and virological condition.
Collapse
Affiliation(s)
- Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, Second University of Naples, Italy
| | - Loredana Alessio
- Medical Center, Centro Sociale ex Canapificio, Caserta; Medical Center, Centro di Accoglienza "La tenda di Abramo", Caserta, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, Second University of Naples, Italy
| | - Luciano Gualdieri
- Medical Center, Centro per la Tutela della Salute degli Immigrati, Naples, Italy
| | - Mariantonietta Pisaturo
- Medical Center, Centro Sociale ex Canapificio, Caserta; Medical Center, Centro di Accoglienza "La tenda di Abramo", Caserta, Italy
| | - Carmine Minichini
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, Second University of Naples, Italy
| | - Giovanni Di Caprio
- Medical Center, Centro Sociale ex Canapificio, Caserta; Medical Center, Centro di Accoglienza "La tenda di Abramo", Caserta, Italy
| | - Mario Starace
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, Second University of Naples, Italy
| | - Lorenzo Onorato
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, Second University of Naples, Italy
| | | | - Margherita Macera
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, Second University of Naples, Italy
| | - Nicola Coppola
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, Second University of Naples, Italy
| |
Collapse
|
35
|
Krishnan P, Pilot-Matias T, Schnell G, Tripathi R, Ng TI, Reisch T, Beyer J, Dekhtyar T, Irvin M, Xie W, Larsen L, Mensa FJ, Collins C. Pooled Resistance Analysis in Patients with Hepatitis C Virus Genotype 1 to 6 Infection Treated with Glecaprevir-Pibrentasvir in Phase 2 and 3 Clinical Trials. Antimicrob Agents Chemother 2018; 62:e01249-18. [PMID: 30061289 PMCID: PMC6153825 DOI: 10.1128/aac.01249-18] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
Over 2,200 patients infected with hepatitis C virus (HCV) genotypes (GT) 1 to 6, with or without cirrhosis, who were treatment naive or experienced to interferon, ribavirin, and/or sofosbuvir were treated with glecaprevir/pibrentasvir for 8, 12, or 16 weeks in eight registrational phase 2 and 3 clinical studies. High rates of sustained virologic response at 12 weeks postdosing (SVR12) were achieved with a <1% virologic failure (VF) rate. The prevalence of baseline polymorphisms (BPs) in NS3 at amino acid position 155 or 168 was low (<3%) in patients infected with GT1, GT2, GT3, GT4, and GT6, while 41.9% of the GT5-infected patients had NS3-D168E; BPs were not detected at position 156 in NS3. The prevalence of NS5A-BPs was high across genotypes, driven by common polymorphisms at amino acid position 30 or 31 in GT2, 58 in GT4, and 28 in GT6. The prevalence of NS5A T/Y93 polymorphisms was 5.5% in GT1, 4.9% in GT3, and 12.5% in GT6. Consistent with the activity of glecaprevir and pibrentasvir against most amino acid polymorphisms in vitro, BPs in NS3 and/or NS5A did not have an impact on treatment outcome for patients infected with GT1 to GT6, with the exception of treatment-experienced GT3-infected patients treated for 12 weeks, for whom a 16-week regimen of glecaprevir/pibrentasvir was required to achieve SVR12 rates of ≥95%. Among the 22 patients experiencing VF, treatment-emergent substitutions were detected in NS3 in 50% of patients and in NS5A in 82% of patients, frequently as a combination of substitutions that conferred resistance to glecaprevir and/or pibrentasvir. The glecaprevir/pibrentasvir regimen, when the recommended durations are used, allows for a pan-genotypic treatment option without the need for baseline resistance testing.
Collapse
Affiliation(s)
- Preethi Krishnan
- Research & Development, AbbVie, Inc., North Chicago, Illinois, USA
| | | | - Gretja Schnell
- Research & Development, AbbVie, Inc., North Chicago, Illinois, USA
| | - Rakesh Tripathi
- Research & Development, AbbVie, Inc., North Chicago, Illinois, USA
| | - Teresa I Ng
- Research & Development, AbbVie, Inc., North Chicago, Illinois, USA
| | - Thomas Reisch
- Research & Development, AbbVie, Inc., North Chicago, Illinois, USA
| | - Jill Beyer
- Research & Development, AbbVie, Inc., North Chicago, Illinois, USA
| | - Tatyana Dekhtyar
- Research & Development, AbbVie, Inc., North Chicago, Illinois, USA
| | - Michelle Irvin
- Research & Development, AbbVie, Inc., North Chicago, Illinois, USA
| | - Wangang Xie
- Research & Development, AbbVie, Inc., North Chicago, Illinois, USA
| | - Lois Larsen
- Research & Development, AbbVie, Inc., North Chicago, Illinois, USA
| | - Federico J Mensa
- Research & Development, AbbVie, Inc., North Chicago, Illinois, USA
| | | |
Collapse
|
36
|
Schnell G, Tripathi R, Beyer J, Reisch T, Krishnan P, Dekhtyar T, Irvin M, Hall C, Yu Y, Mobashery N, Redman R, Pilot-Matias T, Collins C. Characterization of demographics and NS5A genetic diversity for hepatitis C virus genotype 4-infected patients with or without cirrhosis treated with ombitasvir/paritaprevir/ritonavir. J Viral Hepat 2018; 25:1078-1088. [PMID: 29624809 DOI: 10.1111/jvh.12906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/16/2018] [Indexed: 01/08/2023]
Abstract
Hepatitis C virus (HCV) genotype 4 (GT4) is genetically diverse with 17 confirmed and 4 provisional subtypes. In this report, HCV GT4-infected patient samples from Phase 2/3 clinical studies were analysed to characterize global demographics and genetic diversity of GT4 infection among patients treated with ombitasvir (OBV, NS5A inhibitor) plus paritaprevir/r (NS3/4A inhibitor codosed with ritonavir). Among 17 subtypes isolated from GT4-infected patients in the PEARL-I and AGATE-I studies, subtype prevalence by country of enrolment and country of origin suggested that subtypes 4a and 4d were likely circulating in Europe, while heterogeneous GT4 subtypes and a portion of GT4a detected in European and North American countries were likely due to immigration of HCV-infected patients from Africa. The distributions of birth cohort and race were also significantly different across GT4 subtypes 4a, 4d, and non-4a/4d. In addition, phylogenetic analyses of NS5A sequences revealed clustering within subtype 4a which segregated by the patient-reported country of origin and the presence of the L30R/S polymorphism. HCV NS5A sequences derived from GT4a-infected patients who originated from Europe and the United States clustered separately from sequences derived from patients who originated from Egypt, suggesting that genetically distinct strains of subtype 4a may be circulating globally. Finally, NS5A baseline polymorphisms were frequently detected at amino acid positions of interest for the inhibitor-class and OBV retained activity against 37 of 39 NS5A GT4 clinical isolates, with no impact on treatment outcome in the PEARL-I and AGATE-I studies.
Collapse
Affiliation(s)
- G Schnell
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| | - R Tripathi
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| | - J Beyer
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| | - T Reisch
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| | - P Krishnan
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| | - T Dekhtyar
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| | - M Irvin
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| | - C Hall
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| | - Y Yu
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| | - N Mobashery
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| | - R Redman
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| | - T Pilot-Matias
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| | - C Collins
- Research & Development, AbbVie Inc., North Chicago, IL, USA
| |
Collapse
|
37
|
Luxenburger H, Graß F, Baermann J, Boettler T, Marget M, Emmerich F, Panning M, Thimme R, Nitschke K, Neumann-Haefelin C. Differential virus-specific CD8 + T-cell epitope repertoire in hepatitis C virus genotype 1 versus 4. J Viral Hepat 2018; 25:779-790. [PMID: 29397015 DOI: 10.1111/jvh.12874] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/05/2018] [Indexed: 01/06/2023]
Abstract
Virus-specific CD8+ T-cell responses play an important role in the outcome of hepatitis C virus (HCV) infection. To date, most HCV-specific CD8+ T-cell epitopes have been defined in HCV genotype 1 infection. In contrast, the HCV genotype 4-specific CD8+ T-cell response is poorly defined. Here, we analysed whether known HCV-specific CD8+ T-cell epitopes are also recognized in HCV genotype 4-infected patients and set out to identify the first HCV genotype 4-specific CD8+ T-cell epitopes. We studied patients chronically infected with HCV genotype 1 (n = 20) or 4 (n = 21) using 91 well-described HCV-specific epitope peptides. In addition, we analysed 24 genotype 4-infected patients using 40 epitope candidates predicted using an in silico approach. HCV-specific CD8+ T-cell responses targeting previously described epitopes were detectable in the majority of genotype 1-infected patients (11 of 20). In contrast, patients infected with HCV genotype 4 rarely targeted these epitopes (4 of 21; P = .0247). Importantly, we were able to identify eight novel HCV genotype 4-specific CD8+ T-cell epitopes. Only one of these epitopes was shared between genotype 1 and genotype 4. These results indicate that there is little overlap between CD8+ T-cell repertoires targeting HCV genotype 1 and 4. Prophylactic vaccination studies based on HCV genotype 1 are currently underway. However, in countries with the highest prevalence of HCV infection, such as Egypt, most patients are infected with HCV genotype 4. Thus, prophylactic vaccination strategies need to be adapted to HCV genotype 4 before their application to regions where HCV genotype 4 is endemic.
Collapse
Affiliation(s)
- Hendrik Luxenburger
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Franziska Graß
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Janina Baermann
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Tobias Boettler
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Matthias Marget
- Institute of Transfusion Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Emmerich
- Faculty of Medicine, Institute for Cell and Gene Therapy, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Faculty of Medicine, Institute of Virology, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Robert Thimme
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Katja Nitschke
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Christoph Neumann-Haefelin
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| |
Collapse
|
38
|
Uribe-Noguez LA, Ocaña-Mondragón A, Mata-Marín JA, Gómez-Torres ME, Ribas-Aparicio RM, de la Luz Martínez-Rodríguez M. Presence of rare hepatitis C virus subtypes, 2j, 2k, and 2r in Mexico City as identified by sequencing. J Med Virol 2018; 90:1277-1282. [PMID: 29508903 DOI: 10.1002/jmv.25070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/21/2018] [Indexed: 12/21/2022]
Abstract
The HCV 5'UTR, Core/E1, and NS5B regions of samples from fifty patients infected with the hepatitis C virus (HCV) were analyzed. Seventeen patients were identified with genotype (GT) 1b, eleven with GT-1a, nine with GT-2b and four with GT-3a. Two rare subtypes were detected: GT-2j in two patients and GT-2r in one patient. Three patients had mixed infections: one with GT-2k + 2j and two with GT-1b + 2b. This work identifies HCV GTs, 2j, 2k, and 2r for the first time in Mexico.
Collapse
Affiliation(s)
- Luis Antonio Uribe-Noguez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, CDMX, México.,Departamento de Microbiología, Programa en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CDMX, México
| | - Alicia Ocaña-Mondragón
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, CDMX, México
| | - José Antonio Mata-Marín
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, CDMX, México
| | - María Elena Gómez-Torres
- Laboratorio de urgencias, Hospital de Infectología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social, CDMX, México
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Programa en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CDMX, México
| | | |
Collapse
|
39
|
Némoz B, Roger L, Leroy V, Poveda JD, Morand P, Larrat S. Evaluation of the cobas® GT hepatitis C virus genotyping assay in G1-6 viruses including low viral loads and LiPA failures. PLoS One 2018; 13:e0194396. [PMID: 29566005 PMCID: PMC5864039 DOI: 10.1371/journal.pone.0194396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/04/2018] [Indexed: 12/19/2022] Open
Abstract
Direct-acting antiviral (DAA) drug performances depend on the viral genotype. So international recommendations give typing of the virus a prerequisite for treatment choice and patient management. Commercially available HCV genotyping kits are scarce and this analysis is often in-house using tedious PCRs and Sanger sequencing, leading to a lack of standardization. A newly commercialized HCV genotyping assay based on real-time PCR has been developed by Roche Diagnostics (Mannheim, Germany). We compared this new assay with our in-house PCRs -sequencing technique on 101 regular samples and 81 LiPA failures or low viral load samples. No genotype or 1a/1b subtype mismatch was observed. Two samples were misidentified at the subtype level without clinical impact. Three genotype 1b and two genotype 1a samples with low viral load could not be subtyped. Nevertheless, 13 (13%) samples from the regular panel and 35 (43%) from the more difficult-to-type panels failed to give results on first pass with the Roche kit. Failures were mostly associated with genotype 3 subtype a, with genotype 4 subtype non-a, or with viral loads <200 IU/mL (p = 0.0061). The workflow allowed a non-specialized technician to obtain results in less than 4 hours whereas 2 to 3 days and experienced staff were required with the in-house assay. In conclusion, the Roche cobas® HCV GT kit is easy and rapid to use and provides reliable results. The high rate of uninterpretable results particularly for low viral load samples and less frequent genotypes, and the absence of subtyping for non-genotype 1 could require sending complex samples to a specialized laboratory.
Collapse
Affiliation(s)
- Benjamin Némoz
- Laboratory of Virology, Institute for Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
| | - Léa Roger
- Laboratory of Virology, Institute for Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
| | - Vincent Leroy
- Department of Hepatology, Grenoble Alpes University Hospital, Grenoble, France
| | | | - Patrice Morand
- Laboratory of Virology, Institute for Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
- Institut of Structural Biology (IBS) –Mixed Research Unit 5075 (CEA-CNRS-UGA), Grenoble, Grenoble, France
| | - Sylvie Larrat
- Laboratory of Virology, Institute for Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
- Institut of Structural Biology (IBS) –Mixed Research Unit 5075 (CEA-CNRS-UGA), Grenoble, Grenoble, France
- * E-mail:
| |
Collapse
|
40
|
El-Tahan RR, Ghoneim AM, Zaghloul H. 5' UTR and NS5B-based genotyping of hepatitis C virus in patients from Damietta governorate, Egypt. J Adv Res 2018; 10:39-47. [PMID: 30046475 PMCID: PMC6057237 DOI: 10.1016/j.jare.2018.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 01/04/2018] [Accepted: 01/07/2018] [Indexed: 12/11/2022] Open
Abstract
Chronic hepatitis C virus (HCV) infection is a main health problem in Egypt causing high rates of mortalities. Egypt has the highest HCV prevalence in the world, with specific HCV subtypes epidemic and circulating extensively in the country. Different antiviral therapy protocols have been implemented for treating Egyptian HCV patients. Due to the limited data about HCV in Egypt, this study aimed to genotype HCV strains circulating in the Nile Delta Damietta governorate and to investigate the variation in the nonstructural 5B (NS5B) region targeted by the newly approved antiviral drugs. Thirty HCV samples from treatment-naïve patients were genotyped by restriction fragment length polymorphism. Some samples were genotyped by direct sequencing of their 5' untranslated region (UTR) and NS5B regions. Phylogenetic analysis was also performed on the sequences of their NS5B regions. Fourteen new sequences have been deposited in the GenBank database. Results showed that subtype 4a was prevalent in addition to subtype 1g. None of the previously reported NS5B substitutions were detected in the sequenced isolates from treatment-naïve patients, which may be a good predictor for efficient treatment of HCV Egyptian patients with Sofosbuvir. Further studies on Sofosbuvir treated-HCV Egyptian patients are required to investigate whether any NS5B substitutions can confer resistance to treatment.
Collapse
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
| |
Collapse
|
41
|
Krishnan P, Schnell G, Tripathi R, Beyer J, Reisch T, Dekhtyar T, Irvin M, Xie W, Fu B, Burroughs M, Redman R, Kumada H, Chayama K, Collins C, Pilot-Matias T. Integrated Resistance Analysis of CERTAIN-1 and CERTAIN-2 Studies in Hepatitis C Virus-Infected Patients Receiving Glecaprevir and Pibrentasvir in Japan. Antimicrob Agents Chemother 2018; 62:e02217-17. [PMID: 29180522 PMCID: PMC5786793 DOI: 10.1128/aac.02217-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 11/19/2017] [Indexed: 02/06/2023] Open
Abstract
Glecaprevir and pibrentasvir are hepatitis C virus (HCV) pangenotypic inhibitors targeting NS3/4A protease and NS5A, respectively. This once-daily, fixed-dose combination regimen demonstrated high sustained virologic response 12 weeks postdosing (SVR12) rates in CERTAIN-1 and CERTAIN-2 studies in Japanese HCV-infected patients, with a low virologic failure rate (1.2%). There were no virologic failures among direct-acting antiviral (DAA)-treatment-naive genotype 1a (GT1a) (n = 4)-, GT1b (n = 128)-, and GT2 (n = 97)-infected noncirrhotic patients treated for 8 weeks or among GT1b (n = 38)- or GT2 (n = 20)-infected patients with compensated cirrhosis treated for 12 weeks. Two of 33 DAA-experienced and 2 of 12 GT3-infected patients treated for 12 weeks experienced virologic failure. Pooled resistance analysis, grouped by HCV subtype, treatment duration, prior treatment experience, and cirrhosis status, was conducted. Among DAA-naive GT1b-infected patients, the baseline prevalence of NS3-D168E was 1.2%, that of NS5A-L31M was 3.6%, and that of NS5A-Y93H was 17.6%. Baseline polymorphisms in NS3 or NS5A were less prevalent in GT2, with the exception of the common L/M31 polymorphism in NS5A. Among DAA-experienced GT1b-infected patients (30/32 daclatasvir plus asunaprevir-experienced patients), the baseline prevalence of NS3-D168E/T/V was 48.4%, that of NS5A-L31F/I/M/V was 81.3%, that of the NS5A P32deletion was 6.3%, and that of NS5A-Y93H was 59.4%. Common baseline polymorphisms in NS3 and/or NS5A had no impact on treatment outcomes in GT1- and GT2-infected patients; the impact on GT3-infected patients could not be assessed due to the enrollment of patients infected with diverse subtypes and the limited number of patients. The glecaprevir-pibrentasvir combination regimen allows a simplified treatment option without the need for HCV subtyping or baseline resistance testing for DAA-naive GT1- or GT2-infected patients. (The CERTAIN-1 and CERTAIN-2 studies have been registered at ClinicalTrials.gov under identifiers NCT02707952 and NCT02723084, respectively.).
Collapse
Affiliation(s)
- Preethi Krishnan
- Research and Development, AbbVie Inc., North Chicago, Illinois, USA
| | - Gretja Schnell
- Research and Development, AbbVie Inc., North Chicago, Illinois, USA
| | - Rakesh Tripathi
- Research and Development, AbbVie Inc., North Chicago, Illinois, USA
| | - Jill Beyer
- Research and Development, AbbVie Inc., North Chicago, Illinois, USA
| | - Thomas Reisch
- Research and Development, AbbVie Inc., North Chicago, Illinois, USA
| | - Tatyana Dekhtyar
- Research and Development, AbbVie Inc., North Chicago, Illinois, USA
| | - Michelle Irvin
- Research and Development, AbbVie Inc., North Chicago, Illinois, USA
| | - Wangang Xie
- Research and Development, AbbVie Inc., North Chicago, Illinois, USA
| | - Bo Fu
- Research and Development, AbbVie Inc., North Chicago, Illinois, USA
| | | | - Rebecca Redman
- Research and Development, AbbVie Inc., North Chicago, Illinois, USA
| | | | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Hiroshima University, Hiroshima, Japan
| | | | | |
Collapse
|
42
|
Integrated Resistance Analysis of CERTAIN-1 and CERTAIN-2 Studies in Hepatitis C Virus-Infected Patients Receiving Glecaprevir and Pibrentasvir in Japan. Antimicrob Agents Chemother 2018. [PMID: 29180522 DOI: 10.1128/aac.02217-17:] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Glecaprevir and pibrentasvir are hepatitis C virus (HCV) pangenotypic inhibitors targeting NS3/4A protease and NS5A, respectively. This once-daily, fixed-dose combination regimen demonstrated high sustained virologic response 12 weeks postdosing (SVR12) rates in CERTAIN-1 and CERTAIN-2 studies in Japanese HCV-infected patients, with a low virologic failure rate (1.2%). There were no virologic failures among direct-acting antiviral (DAA)-treatment-naive genotype 1a (GT1a) (n = 4)-, GT1b (n = 128)-, and GT2 (n = 97)-infected noncirrhotic patients treated for 8 weeks or among GT1b (n = 38)- or GT2 (n = 20)-infected patients with compensated cirrhosis treated for 12 weeks. Two of 33 DAA-experienced and 2 of 12 GT3-infected patients treated for 12 weeks experienced virologic failure. Pooled resistance analysis, grouped by HCV subtype, treatment duration, prior treatment experience, and cirrhosis status, was conducted. Among DAA-naive GT1b-infected patients, the baseline prevalence of NS3-D168E was 1.2%, that of NS5A-L31M was 3.6%, and that of NS5A-Y93H was 17.6%. Baseline polymorphisms in NS3 or NS5A were less prevalent in GT2, with the exception of the common L/M31 polymorphism in NS5A. Among DAA-experienced GT1b-infected patients (30/32 daclatasvir plus asunaprevir-experienced patients), the baseline prevalence of NS3-D168E/T/V was 48.4%, that of NS5A-L31F/I/M/V was 81.3%, that of the NS5A P32deletion was 6.3%, and that of NS5A-Y93H was 59.4%. Common baseline polymorphisms in NS3 and/or NS5A had no impact on treatment outcomes in GT1- and GT2-infected patients; the impact on GT3-infected patients could not be assessed due to the enrollment of patients infected with diverse subtypes and the limited number of patients. The glecaprevir-pibrentasvir combination regimen allows a simplified treatment option without the need for HCV subtyping or baseline resistance testing for DAA-naive GT1- or GT2-infected patients. (The CERTAIN-1 and CERTAIN-2 studies have been registered at ClinicalTrials.gov under identifiers NCT02707952 and NCT02723084, respectively.).
Collapse
|
43
|
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.
Collapse
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.
| |
Collapse
|
44
|
Abstract
Hepaciviruses and pegiviruses constitute two closely related sister genera of the family Flaviviridae. In the past five years, the known phylogenetic diversity of the hepacivirus genera has absolutely exploded. What was once an isolated infection in humans (and possibly other primates) has now expanded to include horses, rodents, bats, colobus monkeys, cows, and, most recently, catsharks, shedding new light on the genetic diversity and host range of hepaciviruses. Interestingly, despite the identification of these many animal and primate hepaciviruses, the equine hepaciviruses remain the closest genetic relatives of the human hepaciviruses, providing an intriguing clue to the zoonotic source of hepatitis C virus. This review summarizes the significance of these studies and discusses current thinking about the origin and evolution of the animal hepaciviruses as well as their potential usage as surrogate models for the study of hepatitis C virus.
Collapse
Affiliation(s)
- Alex S Hartlage
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205;
| | - John M Cullen
- North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina 27606
| | - Amit Kapoor
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205; .,Department of Pediatrics, College of Medicine and Public Health, Ohio State University, Columbus, Ohio 43210
| |
Collapse
|
45
|
Dirani G, Paesini E, Mascetra E, Farabegoli P, Dalmo B, Bartolini B, Garbuglia AR, Capobianchi MR, Sambri V. A novel next generation sequencing assay as an alternative to currently available methods for hepatitis C virus genotyping. J Virol Methods 2017; 251:88-91. [PMID: 29045810 DOI: 10.1016/j.jviromet.2017.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/17/2017] [Accepted: 10/05/2017] [Indexed: 12/31/2022]
Abstract
Chronic HCV infection is one of the leading causes of liver-related death and in many countries it is a primary reason for having a liver transplant. HCV genotype identification has long been used in the clinical practice, since different genotypes have different response rates and required different doses and durations of IFN/RBV treatment; moreover both the frequency and the pattern of resistance to different Direct-Acting Antivirals (DAAs) classes are subtype specific. Hence the necessity to make an accurate HCV subtyping becomes a fundamental tool to optimize current and future clinical management of HCV infected subjects. In the present study the performance of a next generation sequencing (NGS: based on the Ion Torrent Platform-Vela Sentosa SQ 301 sequencer) HCV genotyping assay has been evaluated. The current method targets a region of the NS5B gene and it is the unique NGS based market CE-IVD assay. As a comparative method a commercial method based on the detection via reverse hybridization of 5'UTR and core regions (Versant HCV Genotype 2.0 Assay, LiPA, Siemens) was selected. A total 207 plasma samples from HCV infected individuals were used. No selection was made for these samples that were submitted for routine HCV genotyping. The results show Vela NGS assay assigns major number of HCV subtypes with respect LiPA. Concerning genotype 1 and 3, the discrepancy of assigned subtypes for LiPA with respect to Vela NGS assay is not relevant (1.8% and 2%, respectively); in contrast, the difference of assigned subtypes for genotypes 2 and 4 is very high (96.6% and 100%, respectively). The resistance mutations data, except for 1a and 1b subtypes, remain scarce; the future relevant challenge will be to identify subtypes-specific drug resistance mutations, which are essential to create highly personalized therapeutic pathways.
Collapse
Affiliation(s)
- G Dirani
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy.
| | - E Paesini
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy
| | - E Mascetra
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy
| | - P Farabegoli
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy
| | - B Dalmo
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy
| | - B Bartolini
- Virology Laboratory, National Institute for Infectious Diseases "L.Spallanzani", Rome, Italy
| | - A R Garbuglia
- Virology Laboratory, National Institute for Infectious Diseases "L.Spallanzani", Rome, Italy
| | - M R Capobianchi
- Virology Laboratory, National Institute for Infectious Diseases "L.Spallanzani", Rome, Italy
| | - V Sambri
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy; DIMES, University of Bologna, Bologna, Italy
| |
Collapse
|
46
|
Limited overlap between phylogenetic HIV and hepatitis C virus clusters illustrates the dynamic sexual network structure of Dutch HIV-infected MSM. AIDS 2017; 31:2147-2158. [PMID: 28692530 DOI: 10.1097/qad.0000000000001592] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE MSM are at increased risk for infection with HIV-1 and hepatitis C virus (HCV). Is HIV/HCV coinfection confined to specific HIV transmission networks? DESIGN AND METHODS A HIV phylogenetic tree was constructed for 5038 HIV-1 subtype B polymerase (pol) sequences obtained from MSM in the AIDS therapy evaluation in the Netherlands cohort. We investigated the existence of HIV clusters with increased HCV prevalence, the HIV phylogenetic density (i.e. the number of potential HIV transmission partners) of HIV/HCV-coinfected MSM compared with HIV-infected MSM without HCV, and the overlap in HIV and HCV phylogenies using HCV nonstructural protein 5B sequences from 183 HIV-infected MSM with acute HCV infection. RESULTS Five hundred and sixty-three of 5038 (11.2%) HIV-infected MSM tested HCV positive. Phylogenetic analysis revealed 93 large HIV clusters (≥10 MSM), 370 small HIV clusters (2-9 MSM), and 867 singletons with a median HCV prevalence of 11.5, 11.6, and 9.3%, respectively. We identified six large HIV clusters with elevated HCV prevalence (range 23.5-46.2%). Median HIV phylogenetic densities for MSM with HCV (3, interquartile range 1-7) and without HCV (3, interquartile range 1-8) were similar. HCV phylogeny showed 12 MSM-specific HCV clusters (clustersize: 2-39 HCV sequences); 12.7% of HCV infections were part of the same HIV and HCV cluster. CONCLUSION We observed few HIV clusters with elevated HCV prevalence, no increase in the HIV phylogenetic density of HIV/HCV-coinfected MSM compared to HIV-infected MSM without HCV, and limited overlap between HIV and HCV phylogenies among HIV/HCV-coinfected MSM. Our data do not support the existence of MSM-specific sexual networks that fuel both the HIV and HCV epidemic.
Collapse
|
47
|
Schnell G, Tripathi R, Krishnan P, Beyer J, Reisch T, Irvin M, Dekhtyar T, Setze C, Rodrigues L, Alves K, Burroughs M, Redman R, Chayama K, Kumada H, Collins C, Pilot-Matias T. Resistance characterization of hepatitis C virus genotype 2 from Japanese patients treated with ombitasvir and paritaprevir/ritonavir. J Med Virol 2017; 90:109-119. [PMID: 28842997 PMCID: PMC6680211 DOI: 10.1002/jmv.24923] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/10/2017] [Indexed: 01/02/2023]
Abstract
Treatment of HCV genotype (GT) 2‐infected Japanese patients with paritaprevir (NS3/4A inhibitor boosted with ritonavir) and ombitasvir (NS5A inhibitor) without ribavirin for 12 weeks in the phase 2 study M12‐536, and with ribavirin for 16 weeks in phase 3 study GIFT II resulted in SVR rates of 72.2% to 91.5%. Overall, 11 out of 125 patients with GT2a and 37 out of 79 patients with GT2b infection experienced virologic failure. The prevalence of baseline polymorphisms in NS3 and NS5A and their the impact on treatment outcome, as well as the development of viral resistance in GT2‐infected patients experiencing virologic failure were evaluated by HCV NS3 and NS5A population and clonal sequence analyses. Baseline polymorphisms in NS3 that confer resistance to paritaprevir were rare in both GT2a‐ and GT2b‐infected patients, while baseline polymorphisms in NS5A that confer resistance to ombitasvir were detected in 11.2% and 14.1% of the GT2a‐ and GT2b‐infected patients, respectively. There was no significant impact of baseline polymorphisms on treatment outcome in Japanese patients. The most common treatment‐emergent substitutions at the time of virologic failure occurred at amino acid positions 168 in NS3 and 28 in NS5A in both GT2a‐ and GT2b‐infected patients. Although there was a higher rate of virologic failure in patients with GT2b infection, the resistance analyses presented in this report support the conclusion that testing for baseline resistance‐associated polymorphisms is not warranted for HCV GT2‐infected patients treated with a regimen of ombitasvir/paritaprevir/ritonavir + ribavirin for 16 weeks.
Collapse
Affiliation(s)
- Gretja Schnell
- Research & Development, AbbVie Inc., North Chicago, Illinois
| | - Rakesh Tripathi
- Research & Development, AbbVie Inc., North Chicago, Illinois
| | | | - Jill Beyer
- Research & Development, AbbVie Inc., North Chicago, Illinois
| | - Thomas Reisch
- Research & Development, AbbVie Inc., North Chicago, Illinois
| | - Michelle Irvin
- Research & Development, AbbVie Inc., North Chicago, Illinois
| | | | - Carolyn Setze
- Research & Development, AbbVie Inc., North Chicago, Illinois
| | - Lino Rodrigues
- Research & Development, AbbVie Inc., North Chicago, Illinois
| | - Katia Alves
- Research & Development, AbbVie Inc., North Chicago, Illinois
| | | | - Rebecca Redman
- Research & Development, AbbVie Inc., North Chicago, Illinois
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Hiroshima University, Hiroshima, Japan
| | | | | | | |
Collapse
|
48
|
Efficacy of response-guided directly observed pegylated interferon and self-administered ribavirin for people who inject drugs with hepatitis C virus genotype 2/3 infection: The ACTIVATE study. THE INTERNATIONAL JOURNAL OF DRUG POLICY 2017. [DOI: 10.1016/j.drugpo.2017.05.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
49
|
Merat SJ, van de Berg D, Bru C, Yasuda E, Breij E, Kootstra N, Prins M, Molenkamp R, Bakker AQ, de Jong MD, Spits H, Schinkel J, Beaumont T. Multiplex flow cytometry-based assay to study the breadth of antibody responses against E1E2 glycoproteins of hepatitis C virus. J Immunol Methods 2017; 454:15-26. [PMID: 28855105 DOI: 10.1016/j.jim.2017.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 11/30/2022]
Abstract
Hepatitis C virus (HCV) infection is a major global public health problem. Early induction of cross-reactive neutralizing antibodies during acute infection correlates with the spontaneous clearance of HCV. Understanding the antibody response in multiple subjects in large-scale studies would greatly benefit vaccine development. To determine the breadth of a polyclonal-serum antibody response, and or, the monoclonal antibodies against the different HCV E1E2 genotypes, we developed a quick and high throughput flow cytometry assay using fluorescent cell barcoding to distinguish cells transfected with different E1E2 sequences in a single measurement. HCV-specific antibodies recognizing conformational epitopes were tested for binding to cells transfected with E1E2 from six genotypes. In this assay, 1500 samples can be analyzed for specific binding to 6 different HCV E1E2 sequences within 8h. Plasma of HCV infected subjects were tested in our assay allowing us to determine the breadth of their antibody response. In summary, we developed a quick and high throughput assay to study the specificity of an antibody response against multiple HCV E1E2 sequences simultaneously. This assay can also be used to facilitate the discovery of novel antibodies, and because other flavi- and picornaviruses have similar intracellular assembly mechanisms, this approach can be used to study the antibody response against such viruses.
Collapse
Affiliation(s)
- Sabrina J Merat
- AIMM Therapeutics, Academic Medical Center, Amsterdam, The Netherlands
| | | | - Camille Bru
- AIMM Therapeutics, Academic Medical Center, Amsterdam, The Netherlands
| | - Etsuko Yasuda
- AIMM Therapeutics, Academic Medical Center, Amsterdam, The Netherlands
| | - Esther Breij
- AIMM Therapeutics, Academic Medical Center, Amsterdam, The Netherlands
| | - Neeltje Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, Amsterdam, The Netherlands; Center for Infectious Diseases and Immunity Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
| | - Maria Prins
- Department of Infectious Diseases Research and Prevention, Cluster of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands; Department of infectious diseases, Academic Medical Center, Amsterdam, The Netherlands
| | - Richard Molenkamp
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Arjen Q Bakker
- AIMM Therapeutics, Academic Medical Center, Amsterdam, The Netherlands
| | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hergen Spits
- AIMM Therapeutics, Academic Medical Center, Amsterdam, The Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Tim Beaumont
- AIMM Therapeutics, Academic Medical Center, Amsterdam, The Netherlands.
| |
Collapse
|
50
|
Zayed RA, Omran D, Zayed AA, Elmessery LO. Determinants of Infection Outcome in HCV-Genotype 4. Viral Immunol 2017; 30:560-567. [PMID: 28731371 DOI: 10.1089/vim.2017.0071] [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] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) infection represents a worldwide health problem and has been for long an attractive point of research due to diversity among different genotypes regarding unique geographical distribution and diverse treatment outcome. HCV is considered a major cause of chronic liver disease and cirrhosis, which leads to liver failure and hepatocellular carcinoma requiring liver transplantation. Of the HCV genotypes identified, HCV genotype 4 (HCV-4) is the least studied. HCV-4 is responsible for ∼10% of HCV infections and is common in the Middle East and Africa; recently it is increasingly prevalent in European Countries. HCV-4 is a continuing epidemic in Egypt, having the highest prevalence of HCV worldwide. "Know your epidemic, know your response" concept necessitates better understanding of HCV-4 characteristics to control disease dissemination and progression, which compromises the life quality of chronic HCV-infected patients. In this review, we discuss the epidemiology, natural history, and treatment options for patients with HCV-4 infection.
Collapse
Affiliation(s)
- Rania A Zayed
- 1 Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University , Giza, Cairo, Egypt
| | - Dalia Omran
- 2 Department of Endemic Medicine and Hepato-gastroenterology, Faculty of Medicine, Cairo University , Giza, Cairo, Egypt
| | - Abeer A Zayed
- 3 Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Cairo University , Giza, Cairo, Egypt
| | - Lobna O Elmessery
- 1 Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University , Giza, Cairo, Egypt
| |
Collapse
|