1
|
Fuentes A, Abu-Dayyeh I, de Salazar A, Khasharmeh R, Al-Shabatat F, Jebrin S, Chueca N, Hamdan FM, Albtoush Y, Al-Shaer OA, Rashid MM, AlMohsen O, Al-Jbour M, Abdelnour A, García F. Molecular characterization of patients with chronic hepatitis C virus infection in Jordan: implications on response to direct-acting antiviral therapy. Int J Infect Dis 2023; 135:63-66. [PMID: 37567550 DOI: 10.1016/j.ijid.2023.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/19/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
OBJECTIVES To investigate the molecular characteristics of Hepatitis C Virus (HCV) detected in patients with chronic HCV infection in Jordan. METHODS The study included 48 Jordanian treatment-naïve patients with active chronic HCV recruited from seven governorates. HCV genotype and the resistance-associated substitutions (RAS) profile were investigated by next-generation sequencing of the NS5B, NS5A, and NS3 regions of HCV. RESULTS "Unusual genotype 4 subtypes" were detected in four (8.3%) patients (4n-n = 1, 4o-n = 2, 4v-n = 1); one patient (2.1%) was co-infected by genotypes 1b+4a. Overall prevalence of NS5A RASs was 38.3% (3% cutoff); genotype 4a showed the highest NS5A RAS prevalence (n = 11, 55.0%). Overall prevalence of NS3 RASs was 21.8% (7/32), all genotype 1a-infected patients. CONCLUSIONS We report, for the first time in Jordanian patients with chronic HCV infection, the detection of unusual genotype 4 subtypes 4n, 4o, and 4v. Baseline RASs in NS5A are frequent, with complex RASs patterns in some of the unusual subtypes. Our data support the need for sequencing surveillance programs in sub-Saharan Africa, Asia, and the Middle East and North African region to monitor response to treatment in these subtypes and to facilitate the World Health Organization's 2030 elimination strategy.
Collapse
Affiliation(s)
- Ana Fuentes
- Servicio de Microbiología, Hospital Universitario San Cecilio, Granada, Spain; Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28046, Madrid, Spain
| | | | - Adolfo de Salazar
- Servicio de Microbiología, Hospital Universitario San Cecilio, Granada, Spain; Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28046, Madrid, Spain.
| | | | | | - Samer Jebrin
- Gastroenterology Subdivision, Prince Hamza Hospital, Amman, Jordan
| | - Natalia Chueca
- Servicio de Microbiología, Hospital Universitario San Cecilio, Granada, Spain; Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28046, Madrid, Spain
| | - Faris M Hamdan
- Gastroentereology Subdivision, Al-Bashir Hospital, Ministry of Health, Amman, Jordan
| | - Yazan Albtoush
- Gastroentereology Subdivision, Al-Bashir Hospital, Ministry of Health, Amman, Jordan
| | | | - Mohammed M Rashid
- Consultant gastroenterologist and hepatologist, Private clinic, Amman, Jordan
| | | | | | | | - Federico García
- Servicio de Microbiología, Hospital Universitario San Cecilio, Granada, Spain; Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28046, Madrid, Spain
| |
Collapse
|
2
|
Goto A, Rodriguez-Esteban R, Scharf SH, Morris GM. Understanding the genetics of viral drug resistance by integrating clinical data and mining of the scientific literature. Sci Rep 2022; 12:14476. [PMID: 36008431 PMCID: PMC9403226 DOI: 10.1038/s41598-022-17746-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/30/2022] [Indexed: 11/16/2022] Open
Abstract
Drug resistance caused by mutations is a public health threat for existing and emerging viral diseases. A wealth of evidence about these mutations and their clinically associated phenotypes is scattered across the literature, but a comprehensive perspective is usually lacking. This work aimed to produce a clinically relevant view for the case of Hepatitis B virus (HBV) mutations by combining a chronic HBV clinical study with a compendium of genetic mutations systematically gathered from the scientific literature. We enriched clinical mutation data by systematically mining 2,472,725 scientific articles from PubMed Central in order to gather information about the HBV mutational landscape. By performing this analysis, we were able to identify mutational hotspots for each HBV genotype (A-E) and gene (C, X, P, S), as well as the location of disulfide bonds associated with these mutations. Through a modelling study, we also identified a mutation position common in both the clinical data and the literature that is located at the binding pocket for a known anti-HBV drug, namely entecavir. The results of this novel approach show the potential of integrated analyses to assist in the development of new drugs for viral diseases that are more robust to resistance. Such analyses should be of particular interest due to the increasing importance of viral resistance in established and emerging viruses, such as for newly developed drugs against SARS-CoV-2.
Collapse
Affiliation(s)
- An Goto
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | | | | | - Garrett M Morris
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK.
| |
Collapse
|
3
|
The European Prevalence of Resistance Associated Substitutions among Direct Acting Antiviral Failures. Viruses 2021; 14:v14010016. [PMID: 35062220 PMCID: PMC8781716 DOI: 10.3390/v14010016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/19/2022] Open
Abstract
Background: Approximately 71 million people are still in need of direct-acting antiviral agents (DAAs). To achieve the World Health Organization Hepatitis C elimination goals, insight into the prevalence and influence of resistance associated substitutions (RAS) is of importance. Collaboration is key since DAA failure is rare and real-life data are scattered. We have established a European collaboration, HepCare, to perform in-depth analysis regarding RAS prevalence, patterns, and multiclass occurrence. Methods: Data were extracted from the HepCare cohort of patients who previously failed DAA therapy. Geno—and subtypes were provided by submitters and mostly based on in-house assays. They were reassessed using the Comet HCV subtyping tool. We considered RAS to be relevant if they were associated with DAA failure in vivo previously reported in literature. Results: We analyzed 938 patients who failed DAA therapy from ten different European countries. There were 239 genotypes (GT) 1a, 380 GT1b, 19 GT2c, 205 GT3a, 14 GT4a, and 68 GT4d infections. Several unusual subtypes (n = 15) (GT1b/g/l, GT3b, GT4k/n/r/t) were present. RAS appeared in over 80% of failures and over a quarter had three or more RAS. Multiclass RAS varied over target region and genotype between 0–48%. RAS patterns such as the Q30R + L31M and Q30R + Y93H in GT1a, the L31V + Y93H and L31V + Y93H for GT1b, and A30K + L31M and A30K/V + Y93H for GT3a all occurred with a prevalence below 5%. Conclusion: RAS occur frequently after DAA failures and follow a specific genotype and drug related pattern. Interpretation of the influence of RAS on retreatment is challenging due to various patterns, patients’ characteristics, and previous treatment history. Moving towards HCV elimination, an ongoing resistance surveillance is essential to track the presence of RAS, RAS patterns and gather data for a re-treatment algorithm.
Collapse
|
4
|
Howe AY, Ceccherini-Silberstein F, Dietz J, Popping S, Grebely J, Rodrigo C, Lennerstrand J, Douglas MW, Parczewsk M, Harrigan PR, Pawlotsky JM, Garcia F, Collaborators SHARED. SHARED: An International Collaboration to Unravel Hepatitis C Resistance. Viruses 2021; 13:1580. [PMID: 34452444 PMCID: PMC8402898 DOI: 10.3390/v13081580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023] Open
Abstract
The advent of direct-acting antivirals (DAAs) has transformed the treatment landscape of hepatitis C [...].
Collapse
Affiliation(s)
- Anita Y.M. Howe
- British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada
| | | | - Julia Dietz
- Department of Internal Medicine 1, University Hospital, Goethe University, 65926 Frankfurt, Germany;
| | | | - Jason Grebely
- The Kirby Institute, UNSW Sydney, Sydney, NSW 2006, Australia;
| | - Chaturaka Rodrigo
- Department of Pathology, University of New South Wales, Sydney, NSW 2006, Australia;
| | - Johan Lennerstrand
- Department of Medical Sciences, Clinical Microbiology, Uppsala University, 75121 Uppsala, Sweden;
| | - Mark W. Douglas
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney at Westmead Hospital, Westmead, NSW 2145, Australia;
| | - Milosz Parczewsk
- Department of Infectious Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, 70-507 Szczecin, Poland;
| | - P. Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, BC V5Z 4R4, Canada;
| | - Jean-Michel Pawlotsky
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Henri Mondor Hospital & INSERM U955, 94000 Créteil, France;
| | - Federico Garcia
- Microbiology Department, University Hospital San Cecilio, Instituto de Investigacion Ibs.Granada, 18012 Granada, Spain;
| | | |
Collapse
|
5
|
Popping S, Verwijs R, Cuypers L, Claassen MA, van den Berk GE, De Weggheleire A, Arends JE, Boerekamps A, Molenkamp R, Koopmans MP, Verbon A, Boucher CAB, Rijnders BJ, van de Vijver DAMC. Transmission of NS5A-Inhibitor Resistance-Associated Substitutions Among Men Who Have Sex With Men Recently Infected with Hepatitis C Virus Genotype 1a. Clin Infect Dis 2021; 71:e215-e217. [PMID: 32055843 PMCID: PMC7643739 DOI: 10.1093/cid/ciaa145] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/13/2020] [Indexed: 12/29/2022] Open
Abstract
The transmission of direct-acting antiviral resistance-associated substitutions (RAS) could hamper hepatitis C virus (HCV) cure rates and elimination efforts. A phylogenetic analysis of 87 men who have sex with men recently infected with HCV genotype 1a placed one-third (28/87) in a large cluster, in which 96% harbored NS5A M28V RAS.
Collapse
Affiliation(s)
- Stephanie Popping
- Department of Viroscience, Erasmus Medical Center , University Medical Center, Rotterdam, The Netherlands
| | - Rosanne Verwijs
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Lize Cuypers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Kristelijke Universiteit Leuven, Leuven, Belgium.,Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Mark A Claassen
- Department of Internal Medicine and Infectious Diseases, Rijnstate Ziekenhuis, Arnhem, The Netherlands
| | - Guido E van den Berk
- Department of Internal Medicine and Infectious Diseases, Onze lieve vrouwe gasthhuis, Amsterdam, The Netherlands
| | - Anja De Weggheleire
- Department of Clinical Science, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Joop E Arends
- Department of Internal Medicine and Infectious Diseases, Universitair Medisch Centrum Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Anne Boerekamps
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus Medical Center , University Medical Center, Rotterdam, The Netherlands
| | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Center , University Medical Center, Rotterdam, The Netherlands
| | - Annelies Verbon
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Charles A B Boucher
- Department of Viroscience, Erasmus Medical Center , University Medical Center, Rotterdam, The Netherlands
| | - Bart J Rijnders
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - David A M C van de Vijver
- Department of Viroscience, Erasmus Medical Center , University Medical Center, Rotterdam, The Netherlands
| | | |
Collapse
|
6
|
Chronic hepatitis C virus infection in the Czech Republic and Slovakia: an analysis of patient and virus characteristics. Int J Public Health 2020; 65:1723-1735. [PMID: 33040165 DOI: 10.1007/s00038-020-01496-y] [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: 04/14/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 10/23/2022] Open
Abstract
OBJECTIVES The MOSAIC study gathered data on chronic hepatitis C virus (HCV) infection and its treatment in various countries worldwide. Here we summarise patient and HCV characteristics in the Czech Republic and Slovakia. METHODS MOSAIC was an observational study that included patients with chronic HCV infection untreated at the time of enrolment. Study collected and descriptively analysed patient demographics, disease stage and viral characteristics. Data were collected between February 2014 to October 2014. RESULTS Among 220 patients enrolled, 51.4% were treatment-naïve. The most prevalent HCV genotype was G1 (78.4%), followed by G3 (19.7%). Higher prevalence of G1 was found in treatment-experienced patients (94.3%) compared to treatment-naïve (63.4%). Most participants (67.7%) presented viral RNA load of ≥ 800,000 IU/mL. Liver cirrhosis was reported in 24.5% of patients. Higher HCV RNA load and duration of HCV infection correlated with the degree of liver fibrosis. Anti-HCV interferon-based treatments were initiated in 88.2% of participants. CONCLUSIONS The study confirmed significant changes in the HCV genotypes partition with G3 genotype rapidly increasing in both countries, with possible impact on the WHO eradication initiative and treatment selection.
Collapse
|
7
|
Douglas MW, Tay ESE, Wang DS, Ong ATL, Wilson C, Phu A, Kok J, Dwyer DE, Bull RA, Lloyd AR, Applegate TL, Dore GJ, Howe AY, Harrigan R, George J. Impact of an Open Access Nationwide Treatment Model on Hepatitis C Virus Antiviral Drug Resistance. Hepatol Commun 2020; 4:904-915. [PMID: 32490325 PMCID: PMC7262285 DOI: 10.1002/hep4.1496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/07/2020] [Indexed: 12/21/2022] Open
Abstract
Direct acting antivirals (DAAs) have revolutionized hepatitis C virus (HCV) treatment, but drug resistance could undermine proposed global elimination targets. Real‐world studies are needed to inform the impact of widespread DAA treatment on antiviral resistance in the community. The prevalence and range of posttreatment resistance‐associated substitutions (RASs) was determined in Australian patients with open access to DAAs through a wide range of prescribers. NS3, NS5A, and NS5B regions were amplified by polymerase chain reaction and analyzed by population sequencing. Clinically relevant RASs were identified using online databases (ReCALL and Geno2Pheno[hcv]). Of 572 samples, 60% were from genotype 3 and 27% from genotype 1a. Ninety‐two percent of people failed a DAA regimen containing an NS5A inhibitor, including 10% with a pangenotype regimen. NS5A RASs were detected in 72% of people with genotype 1 and 80% with genotype 3. For genotype 1, there was a range of RASs across the NS5A region, while for genotype 3, the Y93H RAS predominated (72%). The prevalence of NS3 RASs was higher in people exposed to an NS3 inhibitor (35% vs. 3.9%; P < 0.0001). NS5B resistance was rare, with a single case of sofosbuvir resistance. Multiclass drug resistance was found in 33% of people exposed to both NS3 and NS5A inhibitors. Conclusion: The high prevalence of NS5A RASs among people failing DAA therapy reinforces the importance of specific retreatment regimens, ideally guided by resistance testing. The impact of multiclass drug resistance on retreatment in people exposed to both NS3 and NS5A inhibitors needs to be assessed in real‐world studies. Surveillance for increasing antiviral resistance during treatment scale‐up is essential to maintain the efficacy of current DAA regimens.
Collapse
Affiliation(s)
- Mark W Douglas
- Storr Liver Centre The Westmead Institute for Medical Research The University of Sydney and Westmead Hospital Sydney Australia.,Centre for Infectious Diseases and Microbiology Westmead Hospital Sydney Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity University of Sydney Sydney Australia
| | - Enoch S E Tay
- Storr Liver Centre The Westmead Institute for Medical Research The University of Sydney and Westmead Hospital Sydney Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services NSW Health Pathology-Institute of Clinical Pathology and Medical Research Westmead Hospital Westmead Australia
| | - Dao Sen Wang
- Storr Liver Centre The Westmead Institute for Medical Research The University of Sydney and Westmead Hospital Sydney Australia
| | - Adrian T L Ong
- Storr Liver Centre The Westmead Institute for Medical Research The University of Sydney and Westmead Hospital Sydney Australia.,Centre for Infectious Diseases and Microbiology Westmead Hospital Sydney Australia
| | - Caroline Wilson
- Storr Liver Centre The Westmead Institute for Medical Research The University of Sydney and Westmead Hospital Sydney Australia
| | - Amy Phu
- Storr Liver Centre The Westmead Institute for Medical Research The University of Sydney and Westmead Hospital Sydney Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services NSW Health Pathology-Institute of Clinical Pathology and Medical Research Westmead Hospital Westmead Australia
| | - Dominic E Dwyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity University of Sydney Sydney Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services NSW Health Pathology-Institute of Clinical Pathology and Medical Research Westmead Hospital Westmead Australia
| | - Rowena A Bull
- The Kirby Institute University of New South Wales Sydney Australia
| | - Andrew R Lloyd
- The Kirby Institute University of New South Wales Sydney Australia
| | | | - Gregory J Dore
- The Kirby Institute University of New South Wales Sydney Australia
| | - Anita Y Howe
- British Columbia Centre for Disease Control BC Canada
| | | | - Jacob George
- Storr Liver Centre The Westmead Institute for Medical Research The University of Sydney and Westmead Hospital Sydney Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity University of Sydney Sydney Australia
| |
Collapse
|
8
|
Ceccherini-Silberstein F, Cento V, Di Maio VC, Perno CF, Craxì A. Viral resistance in HCV infection. Curr Opin Virol 2018; 32:115-127. [PMID: 30439589 DOI: 10.1016/j.coviro.2018.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/10/2018] [Accepted: 10/29/2018] [Indexed: 12/27/2022]
Abstract
The introduction of new multi-genotypic direct acting antivirals (DAA) in clinical practice has revolutionized HCV treatment, permitting the achievement of >95% rates of sustained virological response in many patients. However, virological failures can occur particularly if the treatments are sub optimal and/or with too short duration. Failure is often associated with development of resistance. The wide genetic variability in terms of different genotypes and subtypes, together with the natural presence and/or easy development of resistance during treatment, are intrinsic characteristics of HCV that may affect the treatment outcome and the chances of achieving a virological cure. This review explores in detail the aspects of HCV innate and treatment-induced resistance to new interferon-free DAA regimens.
Collapse
Affiliation(s)
| | - Valeria Cento
- Residency Program in Microbiology and Virology, Università degli Studi di Milano, Via Festa del Perdono, 7, 20122 Milan, Italy
| | - Velia Chiara Di Maio
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier, 1, 00133 Roma, Italy
| | - Carlo Federico Perno
- Department of Oncology and Oncohematology, Università degli Studi di Milano, Via Festa del Perdono, 7, 20122 Milan, Italy
| | - Antonio Craxì
- Gastroenterology, "P. Giaccone" University Hospital of Palermo, Piazza delle Cliniche, 2, 90127 Palermo, Italy
| |
Collapse
|